Sorry, had to go to a wake. After a little more investigating, luckily? they didn't break off, although that might have actually been better. I can not run a 2 1/2" bolt all the way in though. I did put a small 3" long pick all the way in and could feel all the threads.
I won't be able to get to it today, but I'll run a tap in and clean up the threads. Then replace the hy-trans and filter, assuming I can get the 2 1/2" bolt to go all the way in.
Thanks for all the help