ya, if the collar and pushrod are damaged, then most likely you have other damage as well. i have my transmission apart right now on my work bench b/c i'm putting an LSD insert in, and its pretty clear that since the gears and everything else are so tightly fit together, that other damage is almost a given. smart route on the rebuild!
as for rebuilding it, you might check out Team Rip Engineering (
www.teamrip.com). they specialize in DSMs and the 3/S trannies. (However, i don't know if you have a VR4 or SL/Base--they no longer rebuild the AWD mtx.) but they do offer a wide variety of services and options for upgraded internals, even taller 5th gears.
if i ever need to rebuild my transmission (God forbid i ever hit a deer!), then i'm gonna have TeamRip do it. i think their price is quite comparable to the place you found.