Dumb question that I gotta ask. Did you remove the stick before trying to slip the boot/bracket back on so that it doesn't catch on the stick mounting bolts?
If not you will have to work the boot past those bolts.
You shouldn't get dirt into the shifter without the boot/bracket if you installed the boot that Hurst supplies to wrap around the base of the shifter. The boot/bracket that bolts to the transmission tunnel keeps crap from coming into the car and also works as a noise isolator.