i believe that boot actually also protects from water splashing or temps, besides noise. try unbolting the boot from the tub and see if it shifts properly because it might actually be the side of the shift hole in the tub is hitting now. but if you unbolt the boot and it works, drive around with it unbolted and see how it sounds. if it doesn;t bother you, leave it unbolted or take it off, it would be your call there
I don't feel like working on anything at this time so i sold my yj.