As you have found out, 2" and especialy 3" body lifts cause more problems than they are worth. Don't bend the shifter, just move the console slightly until it is centered again over the shifter. Even that might not fix it, especially if you also have a transfer case drop which just makes the problem worse. The console is only held in place by a few sheet metal screws so it's easy to move it. Once you have the console where you want it, drill a few new holes in the floor pan (they are small diameter) for the console's sheet metal screws to thread into.
Personally, I'd drop the 2" BL down to a 1" and if you have a t-case drop, get rid of it and install a SYE kit and CV driveshaft which eliminates the need for the t-case drop.