lowell knapp

Hey guys, I lowered the back of my CV transmission in my front wheel drive 02 A4 and replaced the tcm. Put it back in place, filled it up from the bottom plug and now it won't shift when I move the gear selector out of park. Almost feels like it's in between gears, it almost shifts. So my question is, is it possible the gear selector linkage got out of whack when I lowered the transmission, and if so how do adjust this issue? Thanks