There are OEM calibrations for the 0411 PCM that will control a later 4L60E and a 4L80. The early 4L60E uses the same transmission controls (shift solenoid, TFT, power circuits) as the later 4L60E...

My two cents when it comes to emissions, is to try and retain all emissions related equipment from the vehicle in use.

The LT1 / L99 EGR should have the same 5 terminal connector as the LS style...