Popping and stuttering after Efi install and rebuid

The exhaust leak will affect the o2 sensor, which the ecu uses to adjust fueling. So yea it matters. The linkage for the trans is THROTTLE PRESSURE, it adjusts the pressure to the clutches depending on throttle opening. Even if you shift manually, with no linkage you’ll destroy the trans. At least zip tie the lever on the trans all the way forward. But you should put the linkage on it.