well sir,
i had a simular thing happen to mine. all other gears work fine, no noises, no bangs... . just no 3rd and 4th.
what happened to mine was the main shaft busted off right at third gear, but the way it is held in there it stays pretty much in place. even when you open up the top of the transmission. you have to take off the input shaft side cover and then it will tip forward. if its broke there.
if you look in my readers rig pictures i have pictures of the damage and what it looked like.
if you need help or anything let me know. i have the manual from standard transmission. i can and have taken pictures of the pages and emailed them for folks. dont let that thing scare you either. i had never messed with one before and its pretty simple.
you can get rebuild kits from standard transmission, or quad4x4.
you could have busted your shift fork as well... ... . that is what i was hoping for, but wasnt the case. good luck to you.