Yeah I've realised the pistons won't come up to level with the block, but I'm sure messing around with FJ20 rods and a custom pin-height in the pistons I can make a combo that's going to give me the height I need.
Close ratio will be hard to obtain, I'm sure I can work something out but in the mean time I'm going to focus on the engine. Header wise I'm going to go Kameari, once I've worked out flow rates etc in the head I'll be able to narrow my decision down to sizing.
Also a colloquial term for short stroking a motor is de-stroker, you'll find it's used quite commonly
In terms of balancers I'm up to date with them, as you say it'll definitely need to be underdriven.
Obviously this thread is all speculation at the moment and things will only become definite as the build progresses, but I'm just trying to get my head around what is needed for the build in a general sense.
I do in fact have a copy of 'How to modify your Nissan & Datsun OHC Engine', and I'm currently reading it
Thanks for all your help guys, it's much appreciated!