There's a LOT of work required, the PO's have done a good job at making my job bloody difficult!

It really is a basket-case, just basically a rolling-chassis and an engine (well mainly an engine) in boxes.
My question is, I'm missing the majority of the engine bolts including the one's that hold the various major parts of the case together, what pitfalls will I come across if I use stainless bolts with the aluminium - will I have to use anti-seize or anti-gall in the assembly process?
I intend using socket-head stainless bolts everywhere (except the large engine support bolts) on the bike, as it's a cheaper and better choice aesthetically and corrosion-wise, but it's the ones on/in the motor I'm most worried about.
Any info greatly appreciated
Thanks
Paul