Everything is behaving completely normal.
I wasn't aware that it would prevent me from using OTAs. Lol oops. Flashing the stock recovery won't erase anything will it?
To be honest, I'm not sure which files were renamed. I downloaded the nexus 4 tool to use for back ups. When I did I seen an option that renames two files to prevent the custom recovery from reverting to stock once the device is rebooted. So I did that option and flashed the recovery with cmd prompt and adb/fastboot. It does work, because the other times I tried to flash it didn't work and always brought up red triangle.
Do you flash the custom recovery to your devices? If I can go back to stock at anytime the same way I went to custom without losing data then I will probably just keep twrp on it and change recoveries as needed when a new OTA comes out.