OK, so I'm going to do the modification where the engine is lowered in the frame by 50mm.
For the front half of the frame, no dramas - cut the front down tubes and the end of the back-bone where they're parallel to each other, and bob's yer uncle. This much is well documented and understood (by me).
What about the rear half? Once the front's been modified, the rear needs to be modded too. Nobody seems to talk about this bit.
My thoughts are: Add the 50mm to tubes that run from the swing-arm pivot to the top shock mounts, and then add in whatever length is needed to the horizontal tubes to make it all line up again (my guess is that it will be around 35mm of extra length). And then add in a similar length (~35mm) to the swing-arm.
Is there a better way?
The obvious disadvantages of this (need for longer shocks [not longer travel], seat fitment, etc) aren't really a problem for me because I'm fitting an alternative seat, and am getting new shocks, etc.