been away a while, I`m surprised this thread still lasts! Anyway, if I understand correctly, the problem at hand is that the 1000 block is too tall for mounting on the 750 crank. It needs 16mm shaved off, which can`t be done without damage. So, here`s a thought:
Standard Yamaha repair procedure involves removing liners and inserting new ones, on a press (Yamaha says they are not rectifiable). So, what about removing the liners, and then shaving 16mm off the bottom of the block, instead of the top? Then, reinsert liners as if new...probably ground 16mm from the bottom as well. I can`t see why it shouldn`t work, and camchain path should not be disturbed too much.
Never done it, though, so I may be talking nonsense. Please correct me if so!
As for CR woes, there is another approach that I have not seen mentioned here yet. A smaller-than-wanted chamber can be profitably turned into a tuning advantage if the chamber is worked around the valves to increase its volume. The idea is to create a bigger-than-standard clearance between valves and combustion chamber walls, so that the flow area at low valve lifts is no longer shrouded by the walls. This is usually done in many heads, and the limit is (you guessed it...) that removing too much metal will drop the compression too much, and skimming the head a great deal to get it back can bring about valve/piston contact, which means making or increasing valve cutouts on piston tops, which then negates the flow increase, etc., etc. But, starting with a smaller head can be an advantage here. Not easy, though; hardest part is making shape the same on all chambers while retaining same volume!

DF