Just out of curiosity why the change? You've done a huge chunk or work for very little benefit.
As far as the PCM differences.... 01 was SBEC with separate transmission control. (Single Board Engine Controller) 05 is NGC3 (Next Generation Controller generation #3) NGC combines engine control and trans control in one controller. There are significant wiring harness and mechanical difference in the engine.
Honestly this is not a great idea. It's a lot of work and I'm not sure you can get it to work with out serious bastardisation. You would be a lot better off just putting an 01-03 engine in. Mechanically it just drops in... electronically ..... You're pretty close to S.O.L.
