looks like you have got your work cut out for you!!!!
Setup wise, i would definatly recomend r31 running gear, rear LSD and discs as well as front struts and discs... this is sure to keep the engineers happy and give you some good stopping power.
For the gear box you have a few options.. i went with, again, the r31, 'stumpy' gear box as it means you dont have to modify the gear box tunnel and requires minor work to bolt onto the ca engine.
for things like brake boosters and hydraulic clutch setup i bought all that through
www.maddat.com.au, and would highly recomend dealing with them, they also have fitting kits for the ca motor (they have heaps of bits and peices). they can also supply you with the above parts mentioned (running gear ect...), but it depends on your budget, i found it cheaper to source the parts and get them reconditioned privatly.
If you start playing with the engine make sure you dont waste money buying cheap manifolds on ebay and the like, save your cash and spend a bit more for a quality product, its worth it in the long run.
Wheels..... stick to smaller sizes like 15 or 16 inch, once you get bigger you are asking for trouble.