The 750 engine is about 3/8" shorter in overall height, so it's easier to put a 750 engine into a 650 than the other way around. The stroke is the same at 82mm, but the 750s use 6" long con rods, center to center, and the 650s uses 6.5" rods. Shortening the rod with the same stroke moves the max torque point down the rpm range. The factory fitted a larger lift/longer duration inlet cam (Thruxton profile) for more low/midrange torque, and then installed an anemic exhaust cam. If you have the engine apart, get a 1969 or later 650 exhaust cam (.314" lift)....earlier ones will work, but are not nitride hardened. I usually take one from a 71 or 72, which are pretty common. Keep the 750 inlet cam, which uses the STD tappets...this combo works great with open/low restriction exhaust systems. (If you have a 650 hot rod, this works great in them, too). With this set up, you can use the low compression (8.5 or 7.9 to one, depending on year), but I like the MAP 9.5 forged pistons. I would consider rebalancing with any aftermarket pistons, or if you have overbored more than .020".
This is a little more complicated, but if the bike is light and the gearing not too high, you can take a light flywheel from a 66-68 650 and replace the heavy flywheel on the 750 crank, then rebalance the whole assy. This makes for a snappy engine, but not for heavy bikes or for mostly two up riding. For a barhopper/bobber solo/streetfighter it makes an interesting combo.
I like a light valve train (tappets, pushrods, rocker arms, adjusters, nuts, spring retainers, valves) for less wear and tear and snappier performance.
The later (mid 73-on) uses the oval port oil pumps, which are the highest output standard pumps readily available and will retrofit into all unit engines.
The 750s also use heavy cam pinions, which act as flywheels to smooth out the cyclic pulses of the cam lobes induce in the valve train. I would use these in either 650 or 750s and I believe you will have better valve train life. The piston type oil pump also causes a pulsing, as it is driven by the inlet cam pinion nut.
I have found more instances of clutch problems and broken gearbox mainshafts in the 750s, moreso than with even hotrodded, 750 kitted 650s which make more horsepower and torque. I suspect the triplex primary chain moves the center of effort outboard just enough to affect the loading on the clutch assy. and mainshaft. Easy fix, if you have a triplex sprocket and clutch....just use a duplex 650 chain fitted to the inner two rows of teeth. This also lightens up the primary drive.
If you have access to a lathe, you can make four top bolts for the rocker boxes that are like the 750 bolts from the rocker box surface down, and like the 650 from the surface up....you need a stud or a threaded hole in the 3/8" thicker bolthead. I would make it with the stud, as it's stronger and you are less likely to strip threads. This will greatly facilitate the installation and allow you to keep the stock top stays.