Thanks for everyones advice so far, and sorry I haven't updated this sooner.
A few things have changed in the last few weeks. 
First big change is I now have a W2A intercooler from frozen boost. 
I have decided to split my 5sgte build into 2 parts. the 5S will still get built but for now I have a 3S getting put together. The reason to do this is to use parts that I already have, saving money initially, get my car running again with this 3S an build the 5S once I'm driving again.
Bottom end is getting put together as I write this.
Includes: 3S gen 2 block
Ross forged 1mm over pistons
New Rings
Eagle Rods
ARP Crank Studs
ACL bearings
Gen 3 MLS head gasket
New oil and water pump.
Standard head, Standard cams.
Walbro 255lph pump 

Sorry didn't get to finish above post.
I have another set of choices to make. (You're all going to be sick of me soon)
Turbo: I have a Hi-flow ct26 and a Garrett GT3076R with 0.82 A/R T3 exhaust housing. I'm thinking put the Garrett on the standard manifold with an adapter and sell the hi-flow.
I have the set of HKS cam gears I can put on, (is it worth it?)
I have a standard ECU and a SARD ECU and the Haltech E8. I'm thinking the SARD to start for simplicity.
Also have a light flywheel for it.
Do I also put the 720cc injectors and fuel rail on it too? Is the SARD ecu capable of this?
 
Best this is, it's all happening. Just designing brackets for this W2A and remote oil cooler at the moment.

I know this thread is old now though make sure you don't buy Ferrea oversized valves. Go with Supertech instead.
The Ferrea valves are faulty.

Hope you lot don't mind some ignorant questions- hows the block height between the engine? How about the OEM compression height of the pistons? Seeing the 3S rods can be used and assuming the same compression height that would suggest it's 2.5mm taller.
 
Going off what I hear about 3S engines wearing out the sides of pistons it would be a good idea to move the pin higher to help offset the rod to stroke ratio.
 
Too bad a Beams head can't be bolted on to a 5S block due to the lack of VVT oil feed, I have however wondered about the option of put a plug in the head and feeding it externally. This is getting off topic though.