Is pounding on my output shaft bad?

I have this really bad thumping from my transfercase at anything over 40mph, and I seem to remember when i was puting in my transfercase I had to be rough with it and use a mini sludge to get it to slide on the output shaft cause it was sticking, it all fit on fine and i have a tumping vibration <40m mph. I had bought this car with out it on so i had no idea if it did it before me. If it is ruined do i have to take out the tranny?