Our '99 Rodeo also goes "clunk" a bit when stopping. I figured it was shocks/struts as our Ford Taurus did the same sort of thing when it's struts were worn. But with only 50k miles I would have hoped that an SUV would have had stouter shocks.
As for the tranny and shifting hard - same here. But another thread in this forum suggests that this might be the gear selector or mode sw. Seems they "fail" when they get hot. (just repeating what I've read here, don't know yet).

When checking the trany fluid the manual I have says to check when between 95? and 130?, and to use the special Isuzu tool to do this with. But of course Harbor freight has a thermocouple meter for less than $30 that does the same thing.