How is the JK's factory wiring and computer handled during a MoTech Gen V LS swap — is the Jeep ECM removed?

Here is what the documentation says. Each point links to its source; details depend on your exact computer, harness and transmission.

• E92; LT1, LT4, L83; 2014+: Gen V E92 ECMs are identified by a sticker on the backside of the module with 'E92' at the top center. Chevrolet Performance LT1/LT4 controller kits ship with a pre-programmed E-92 controller plus fuel pump power module and fuel pressure sensor for direct injection, calibrated for older-vehicle retrofits with unneeded production-vehicle features turned off. (LSX Magazine)
• E92; LT4; 8L90E: Chevrolet Performance LT4 controller kits (e.g., 19419241/19418595) bundle the pre-programmed E-92 controller, harness, sensors, throttle pedal, fuel pump power module, and fuel pressure sensor; there are variants for analog vs digital fuel pressure sensors and a 3-pin variant (19419242) for 8L90E transmissions. (Pace Performance)

Confirm against the instructions for your exact parts before wiring. More: Computer and tune in our tuning guide.