I'm not sure that I completely understand your question.
Are you using the CNCFusion conversion kit? If so, are you saying that you think that the dimensions of the motor mounts supplied by CNCFusion force the motor shaft too deep into the Lovejoy couplings? If that is the case, perhaps it is necessary to put some shims between each motor face and its motor mount to move the shaft back a bit (or else, as you have suggested, you could cut the shaft end).
I have been considering getting that kit, and I have a set of Keling 381 oz-in. motors, but I was thinking of getting some Oldham couplings from McMaster Carr to use instead of the Lovejoys. But since I haven't actually installed the kit, I can't answer your question based on first-hand experience.
However maybe I am misunderstanding the problem that you have encountered.