It sounds like a fun project and the fact that it belonged to your dad is cool. I restored my father-in-law's BMW after he put about 200K on it and then let it sit for about 15 years.
I think you'll be surprised by the performance of your bike. It might just be a fun little track bike if you get it handling good. Speed is a relative thing and going 60mph on the 350 will be a lot more fun and interesting than going 100 on an R6. I learned a long time ago that going fast on a slow bike is more fun than going slow on a fast one. You'd rarely get a chance to really open up an R6 but you'll be able to flog the 350 without going to jail.
As for the cost, the obvious things such as bars,seat,tank,exhaust,etc. are easy to calculate. It's the seals, bearings, cables, shocks, fork springs, tires, tubes, fasteners,carb kits, and the heaping pile of rubber bits that will bite you squarely in the right rear pocket.
Just do a little at a time if you have to and plan your orders to save on shipping. As far as the expensive pieces go, a little research and ingenuity can go a long way. Watch CL and Fleabay for deals. You might even find a project bike on CL that someone has given up on and just wants it gone. I missed a CB450 a few months ago that was already disassembled and he had bought a cafe seat, tank, and numerous other bits and pieces for $500. I didn't look at CL that morning and it had just sold when I called.
