Are we talking about the premium, current model (for each given model year) R6, or are we talking about the R6 "S" which was the old model that continued to be sold for a while alongside the new one?
If we are talking about the current, new model for each respective model year then the answer is simple, "NO". The 2003 R6 is too different from the 2006-onward models.
YES, you can make anything fit anything else, given enough cutting torches, sawzalls, TIG welders, and machine tools.
Engines don't have to be replaced you know, they could be fixed.
I assume you're looking at the ad currently up in the for sale forums... I'd offer the guy $3500ish and then try to fix the motor. Worse comes to worst, just keep your eyes peeled for salvage or wrecked R6s of the same generation and go from there.