Some t-case shifter brackets are designed better than others and those that aren't designed so well can create more problems than they are worth. It sounds like you got one of the latter types, what brand is it? Some report they never get their shifters working properly after installing a shifter kit. And some have no problems shifting at all after installing a body lift and t-case drop without installing a shifter relocation bracket, I was one of those. So with your problems, you might be better off removing the bracket which is probably what I'd try next.
What brand shifter bracket did you install?
Does anyone on WF have any recommendations for a good brand of t-case shifter bracket that works well? With no personal experience with them, I can't make a personal recommendation for any particular product though he may be better off without one if his TJ is anything like mine was when I had a t-case drop and a body lift.
One brand of t-case bracket I have seen recommended a lot is from Advance Adapters, those that use it swear by it.