Thanks for all the help guys.
I'm using Sober's Mega Mod from this thread:
http://www.subsim.com/radioroom/showthread.php?t=192374
I went ahead and did a full re-install, and the sonar guy got his hearing back. I had actually been using an old SH5 patcher that was installed with JSGME, and accidentally uninstalled it while adding the other Mods. I have since been able to download the latest patcher, which happens to be a corrupt zip file. But I figured out how to get the files needed out of it. So I re-installed, updated to 1.2, ran the patcher, then installed the mods using Sobers mep file. I started the new campaign per the instructions, and played for about 3 hours til I got a CTD. Hopefully that was just a fluke.