The body kift is the reason it wont shift correctly.  The floor is getting in the way be9ings basically the hole isnt big enough anymore.  If you get a short throw shifter kit for the trans and t-case it'd solve your issues or you could either bend the shifters to clear or chop the hole in the floor larger to allow proper movement.  Personally Id just bend them. Put a piece of tubing over the handles and bend them.  Its simple and no it wont hurt anything.