yes you use the same boot. no you dont reattach the top. why? i dont know. i would prefer it. i was thinking about grinding out the center on the top thing to make it fit but i have to steal a dremel first
the trd **** sucks i gave it a month and still hated it i encourage you to not bother with it either. the stock one is the best. and yeah the boot on mine is just folded down. id rather have a more "finished" look as it is a TRD kit and i would expect something more complete. as far as everything else i do like the sport shifter its more direct and crisp feeling and still think it was worth it.
on a side note the obx shifters suck as well. when i first test drove the car they(both dealers i test drove at) had them equipped (one had the fatboy the other had the skinny one) its pathetic to sell something at the dealer as UPGRADE equipment that has nowhere near the quality of the stock item.