Get you money back, get your engine back and take it to Precise Engine Rebuilders in Southport (speak to precisegrak on the forums here). Domma_aw11 has these guys do all the work on his hicomp natro with big cams and was very happy with their work.

Wow man I just read the last 4 pages or so...what a mission! I'm glad I didn't go through with a rebuild on my MR2 before I sold it. Just seems like wasted money after seeing all but a few make it back on the road in one piece. Definitely get your money back or at least a large % of it and take it somewhere else. I'd personally be laying down the wrath of god on this engine builder if I was in your position.
 
Engine being stripped for the 3rd time is ridiculous and clearly shows how incompetent this current builder is. I have nowhere near the technical knowledge you do but I know a crowbar pointed in the right direction will get some work done quick smart.

I'll be going to turkey for a month and I told him the date id be back, i told him to have the engine finished by that day. If thats not followed I'll have to get the lawyer involved. If I knew it was going to take this long and be such a prick I would have built a 3sgte instead. 

So who wants to convince me to do a turbo conversion?
 
I wan't to keep my S54 gearbox with the quaiffe though.
 
 

S54 with a turbo engine is not a good combo I am led to believe. With that much more power wouldn't S54 ratios f** up and can it handle it? On the contrary you could give me your quaife :P

I haven't looked very far into it, but there are 3sgte engines running around mated to S54 gearboxes. My s54 has cost an arm and a leg to rebuild and fit lsd. Thats why id like to stay s54, that and all the driveshafts and hubs that could stay the same. 

V6 that shiz then.

if i were to do anything it would have to be over the summer/start of next year, I wan't to drive on the built NA for a while when i get it back. Ill make a plan for the options. I've always been keen on the idea of a V6 but unless you go 2GR theres isnt a lot of power to gain? 

Only other "easy" options I see for you besides the built N/A are turbo or 2GR, even then the 2GR still might have to do a bit of hw. If it's tubby route make sure it's anything above gen 3 as you probably know. If 2GR maybe worthwhile reading up on twobrutal, their working on a 6 speed . But yeh all depends on your power goals I guess.
Maybe drive the standard N/A for a while as you rack up ze funds. You kinda missed out on driving the car all this time :)

I'm making a conversion report/plan. Im going to research each option and see if i can justify it. I think 3vz will be the cheapest and most common swap option.