Oh my goodness! Thank you so much! It has worked as directed, took me a bit longer because I didn't follow the directions as is. For those of you who may also face this problem I've copied the directions down below formatted a bit more cleanly.
[with credit to user pjim]
Use the HTC Tool Kit from here
. You may already have it installed because this is how you likely rooted your phone.
1: Go into Recovery and Format system.
2: Still in recovery, go to "Install Zip" then choose "Install zip from sideload"
3: Use the Toolkit to flash a ROM that could be smaller than 900mb by going into the "ADB" button and then choosing a ROM from the File Path, then clicking "Sideload"
4: Once it's finished installing, let it boot, and let your phone boot into the password screen as well.
5: Power back down and then go back into Recovery.
6: Go to the "Mounts and Storage Menu," scroll down and then select "format /data and /data/media (/sdcard)"
7: Reboot into a new clean phone.
Extra note: Make sure you always back-up your data in case of problems that arise like this! Although I have a feeling that this may have also arisen as a result of having S-ON, so maybe doing S-OFF should prevent this, though I could be wrong.