Proper transmission/transaxle and engine alignment are vital to a vehicle's driveability. Misalignment causes undue stress on the input and stator shaft, the torque converter, and the flexplate. It makes the oil pump's bushing and seal wear prematurely.
Transmission housings are cast aluminum cases that contain the internal components and protect the transmission from damaging dirt and debris. Dirt causes transmission bushings and bearings to fail, resulting in shaft misalignment, friction disc, oil pump failure, and more. Fine metal debris caused by a spun oil pump bushing can spread throughout the transmission coating components, sticking to solenoids and clogging filters and passages.
Measurements with a dial indicator mounted to the crankshaft are taken. Shifting the bellhousing or inserting offset dowl pins can often correct bellhousing misalignment.
Pinching electrical harnesses and wiring between the engine and bellhousing affects alignment and also creates circuit problems.