Thanks Tony, yep, definitely replacing valve seals.  I'd ordered SuperTech viton seals, any good?  If sus, any suggestion where I get the GSC seals?  I like your comment about MegaSquirt and I'll stick with stock ECU!  I'll get the stock injectors checked as you suggest.  Thanks

Supertech valve seals are good too, same as gsc in terms of quality I hear.

Injectors cleaning, depends what state you are in and what you want to spend, as example, Brisbane injectors does clean and flow test (basic) and around $120 (with new isolators/rubber orings), Injectors Online has more advanced equipment and Melbourne charges around $150 (orings separate).
Toyota did a good job for it's time of an ecu, up to 16psi +or- (afm), for 440/540cc injectors, all ge and gte gen camshafts, on high Ron fuel.
Consider an adjustable fuel pressure regulator to get a little more out of your 440cc or even if you go gen 3 / supra 540cc. Your rods, pistons, head gasket, ecu, etc can make more hp / boost than your injectors. Again won't be an ideal fuel trim in todays engineering terms but will run great and safe when pushing out a little more hp.

Big thing high on the list IMO is getting your side fuel rail bored to minimum of 6mm, ideally 7mm. Machinist on the gold coast (mb engineering) has a custom made drill bit charges $200. 3sgte gen 2 is known to be very lean in centre / end cylinders for a few reasons, main issue is side feed rail. Demonstrated in the parts engineering. Gen 2 440cc injector vs gen 3 540cc aka an increase of 23 percent. Stock gen 2 rail is 3mm aka area of 7, stock gen 3 rail is 6mm aka area of 28, aka an increase of 300 percent. Some aftermarket research was done in the early 2000s and concluded based on the rail a bore of 6mm-8mm should be done on gen 2 rails with stock injectors (depending on injector size and machine used to ensure doesn't crack the rail).

Lots of info out there, read around, chat with other owners.

Thanks Tony, I found that analysis, http://www.wolfkatz.com/Articles/WolfKatz%20Fuel%20Rail%20Test%20Final%20Report.pdf. Very interesting how the 3SGTE evolved from the gen II to gen III.  I'd seen how they simplified intake manifold vs turbo boost but this restriction in the fuel rail is very subtle and seems to have been pretty significant.  I note that the plug in my gen II rail is 7mm diameter.  Does this indicate that someone has been in there already or is this the std plug for even the 3mm bore?  Can you send me contact details for mb engineering, I couldn't find anything on them.  Something out there on Road & Track Ipswich maybe doing the same thing but I like the idea of someone with a custom drill bit as this rail casting looks pretty fragile.  Would it be better to try and chase down a gen III fuel rail, are they compatible with my gen II head and manifold?

No Gen 3 has different offset of injector.
Take injector out and look at bore of the rail.
Send you a PM than getting away from your build thread.

Valves now reseated and cylinders honed.   Then out to a truck power cleaner bay with degreaser and the various bits, head, manifolds etc to make sure that there is no grit left anywhere.  I zip-tied a protective sheet to the block side of the head so that it wouldn't get bumped as the power cleaner can move things around.  Also helps to tie parts down before applying the jet.
 
So now waiting on new parts to come in.   I will then be getting into gaskets and sealing.   I noticed that the previous rebuild of this engine didn't use any gasket between the oil pan and block, only sealant.  I also noticed little bits in the MR2 manual where they put a bit of sealant in corners of seals like the rocker cover corners.   What is the latest thinking about the oil pan sealing, I know that this can be a problem area.  And any other sealing tips I could use?  I'd hate to get it all together and then have oil leaks!

All parts here - checked clearances of new main bearing and big end shells with Plastigage to confirm that they and the crankshaft were within spec.
 
Cleaned up the head and block gasket mating surfaces.  The Cometic gasket specified an RA50 smoothness factor which is a higher smoothness than conventional gasket technology.  This is equivalent to what you might achieve with 150 grit paper and I felt that I’d finished the head and block to better than this however, seeing as I am not going horsepower I bought a conventional Permaseal head gasket.  Conventional gaskets seem to be more tolerant of surface finish than the Cometic.  The finish of the head gasket that came with the Domestic Gasket kit was much rougher than the Permaseal gasket.  The Permaseal gasket was the same design as was in the engine when I dismantled it. 
 
Reground the inlet and exhaust valves and got a nice even ring sealing region on all valves.  I cleaned the valve springs and caps etc as there was a lot of oil residue in the head.  Lubricated the springs afterward as there is some talk about corrosion of springs can lead to spring failure.
Honed the cylinders and gave the block and head a good wash at the local truck pressure wash station.
The Domestic Gasket Ebay advertisement showed NPR rings however the supplied rings were branded Evergreen. I fitted the supplied piston rings to the bores to check ring gap and the top and middle were Ok however the oil control rings looked too large.  So I bought some Hastings rings as backup.  
 
I wondered about reusing the clutch and bit the bullet and bought a new Exedy TYK-7248 clutch and had the flywheel resurfaced.
 
I used my dad’s sturdy old drill press and a wooden jig to press out the little end pins from the old pistons.

New pistons fitted and ready for rings.  The cable ties were reminders as to 1, 2, 3, 4.  As well as marks on conrods etc!

 
I didn’t like the special nuts on the ARP big end bolts and wasn’t sure about pressing out the existing rod bolts so decided to reuse the existing rod bolts.  I’d checked forums and it seemed that this wasn’t unusual.  Not like the one-time head bolts etc.
 
So much for smart decisions.  One of the rod bolts fractured before reaching specified torque.  So so lucky that this didn't happen after assembly!  The next pic shows the fracture, just under the head.  The crack has been there a while as it has an oily black coating.  The last region that was holding the bolt head is the fresh grey fractured face in the red circle.  Odd how these bolts have a taper below the head, it seems to be a stress concentrator.   The ARP bolts don’t have this tapered neck.

So I found out how to press out the rod bolts, bought the special 12-point socket for the ARP nuts , pressed in the ARP bolts, and went through the ARP rod bolt assembly process, lube etc.
 
Next shows pistons on rods, ready for assembly.

 
OK, block ready for head, now for head assembly.

The seals that were supplied by Domestic Gasket were in an Evergreen outer bag with an inner bag labelled “Valve Stem Seals Viton Material”.  I wondered about using some of these Viton seals in  place of the SuperTech polyacrylate(?) intake seals however the mouldings of the Evergreen seals looked a bit rougher than the SuperTech seals so stick with all SuperTech.
 
I made a wooden jig for the head assembly that significantly helped me with the valve spring retainers.  The valve stem was vertical and the retainers much less likely to fall out and disappear somewhere never to be seen.  I had to buy further retainers after initially making this mistake.
 
 
 
The new Toyota V6 valve buckets arrived and looked great.

 
However they were different to the 3SGTE buckets in that the surface between the shim and the valve stem was thinner by about 0.18mm. This meant that I either gave up on the V6 buckets and looked for some 3SGTE buckets or bought a number of thicker shims. Seeing as I expected to be buying some new shims even with the 3SGTE buckets I went with the V6 buckets and new thicker shims.

Assembled valves, spring seats, springs (note there is a top), spring caps, and retainers.

Then attached the head to the block. It seems that Toyota don’t want you to fit camshafts before the head is attached/supported by the block. So you can’t do valve clearances until the head is attached and the camshafts then mounted.

After measuring valve clearances with the original 3SGTE shims (this is when I found the issue with thickness of the v6 buckets) I was able to calculate what shim thicknessed I needed and order them. Only one wasn’t ex-stock and I was able to go to a neighbouring value and still have clearance within spec. I fitted the shims and turned the camshafts over a couple of times to remove any slack and all but two exhaust valve gaps were within spec. The exhaust specifies 0.2 to 0.3mm and we have two at 0.31mm. The gen III spec went out to 0.38mm so we should be OK. Better 0.1mm too open than too tight.

Next was to fit the oil pump, water pump, pulleys, timing belt etc. One of the timing belt tensioner mounting bolts turned out to have pulled some threads out when I removed it. Seems like corrosion of 30 year-old alloy not good. Fortunately this bolt was the outer mounting bolt and I was able to fit a through bolt and nut.

Fitted the oil pickup and oil pan. The gasket kit came with an oil pan gasket however there are lots of warnings on forums to discard these and go with the Toyota FIPG gasket sealant which I did.

Camshaft cover fitted. Delivery pipe, injectors, TVIS and inlet manifold fitted. COMETIC MLS gasket for exhaust manifold not so good. The instructions say that the brass riveted points must be outside the compressed region however they are not. I contacted COMETIC and they said that I could remove the brass rivets if I was able to align the layers. The studs did a very good job of this together with finger pressure on the bottom edge of the gasket. This also gave better alignment of the COMETIC gasket around the exhaust ports.

Only needed to make one custom gasket and it is in a pretty low-stress area on the intake manifold.

 
I had an aftermarket CT26 turbo with low use and the axial play looked pretty good at only 0.11mm so I went with this.  Being able to invert the engine on the engine stand made the turbo much easier to install.  I don’t know how people do this with the engine in the car!
 
I’ve fitted a cheap oil filter that I’ll swap out after only a few km.  And some old plug lead bits as dust covers until I install the plugs.  Still a mess of hoses to go but looking like an engine and ready for the car. 

 
 
 

Amazing thread. 
 
I wonder if you've considered putting in a slightly higher spec turbo? You said it was an aftermarket CT26, does this mean the compressor wheel has been swapped out or do you have any other info on it? I presume you've decided against a CT27 from ATS Racing?
I'd be interested to hear your thoughts about this aspect. 
Good luck with the rest of it, good work mate, I am watching eagerly. 

It's a conventional CT26 turbo in the picture.  I fitted it to check out the plumbing - make sure I hadn't lost any bits etc as it may be a few months before I get the time to haul out the existing engine.  Winter also not helping motivation. I've got a Mamba CT26-GT3071R turbo in the car at the moment and it's only been in a couple of years and not a lot of kms.  The Mamba has an adjustable actuator and some spring options for higher boost than the CT26.  I'll check the Mamba when I remove the engine and may go with that.