Hemi Alternator Wiring

Does anyone know if there's a difference in the internal wiring/function between the 03-08(early) and the 09- newer(Eagle) alternators? Had to switch engines in my son's Scamp. Replaced the 04 with a 2012 5.7. Has the car front accessory drive. I wired the "early" alternator like the old square backs. Two wires out of the back, then into the voltage regulator. Yes, I know. Higher output will burn the car down. Well, when we put the newer engine in, we had to use an appropriate alternator for the year. The spacing is different between the two. So, when we wired in the new pigtail for the alternator, and plugged it in, it Waaaaaay over charges. So much so, that it pulls the engine down. Rev it up, belt squeels like a pig! So, that's my issue. Any thoughts FABO? I should also mention, tried new regulator, grounded properly. Thanks, all!