The chain between the crank and the transmission in these bikes has a hydraulic tensioner, activated off of oil pressure. So when the engine is cold or a low idle it tends to rattle. That may be it. If so, nothing to worry about.
I believe they are the same, at least they are on all the cb750s I've worked on. Got to Partzilla, find the intake boots and look at the Related Fitment section to see what other models they fit.
I would just keep them for now. The other CB750s that have spoked wheels have a single disk brake upfront and a drum in back, so you have that to contend with. The disk brakes on your super sport are fare superior.
I have a set Cruzinimage pistons on my 75 cb750, they are actually pretty darn good. Sure you can get better from say cyclexchange or Ape, but unless your building a race bike you can't beat Cruzinimage
Granted I haven't done the laydown on my 81 cb750, I have on other bikes. I use a bunch of scrap wood to get then engine off the floor and level on it's side. As for the long bolt with the foot pegs, you don't have to mount the foot pegs right away. Often I just put a couple of the engine mount...