As for my issue, it looks like I fixed it once again. I still can't get into the service menu or most of the other hidden activities via the dialer, but I'll have to figure that out later.
And the solution seemed to be simply dicking around in the /efs directory. I noticed one file in particular, named serial_no or something similar. It contained all 0's. So I replaced the contents with my phone's serial number.
I also changed the contents of /efs/carrier/HiddenMenu from OFF to ON. Still didn't fix the dialer codes issue, but I left it with ON, because why not?
I also had some problems with factory mode being on when I flashed the stock firmware, but I dicked around with /efs/FactoryApp and that seemed to work. I had to run the following in the terminal:
echo -n ON >> /efs/FactoryApp/keystr
echo -n ON >> /efs/FactoryApp/factorymode
chown 1000.1000 /efs/FactoryApp/keystr
chown 1000.1000 /efs/FactoryApp/factorymode
chmod 0744 /efs/FactoryApp/keystr
chmod 0744 /efs/FactoryApp/factorymode
So right now everything is back to normal. On the 9/11 CM nightly and no service dropouts at all.
One question though:
I've since ran some diagnostic tools, and one of them said that my phone doesn't have a CSC version, a CSC country, or a PDA version. Could this explain why I can't run any dialer codes?