The gen 2/3 electronics are not a direct swap; the gen 3 runs staged (8) injectors, while the gen 2 runs just 4. The harness and ECU will be different, as well as the TB's, airbox, tank, and fuel rails. Staged injection is superior to the 4 injector set up, but not enough to warrant the change IMHO.
As far as the motor goes, they are nearly identical. The gen 3 has a couple cosmetic changes and different cams IIRC, but is otherwise very similar. There may be other small differences in the head/valves/static compression, but nothing that prevents them from being mechanically interchangeable. If you are in the business of tuning or doing top end work on these motors (which you said you've already done), there's no notable difference between the two.
Attack life... it's going to kill you anyway.