What kind of vehicle is it? Usually, installing a 2" spring lift doesn't necessitate lowering the transmission. Did you try running it before lowering the tranny plate? If not, you might want to try that. Usually, the driveline angle isn't bad enough to do that until you add 3" or 4" of lift.

I also agree that it's likely that your shifter is hitting the edge of the hole in the floorboard, or the hole in the boot ring.

1977 CJ-7, fiberglass body, AMC 360 w/ headers, DUI ignition, Edelbrock intake and Holley 4150 carb, TF999, Dana 300, 4.56 gears lockers, York air comp, 4" susp lift, 2" body lift, BFG 35" M-T tires, Megashifter, AGR pump & box, REP8000 winch.