The full ota has new touch panel code that is not recognized in non stock roms. If you have the latest twrp, it has been updated to work with the new tp code.
Some of us have upgraded using firmware without the tp bits and can, i assume, still run aosp roms. I guess i ought to try it to see.
It looks like there is a flash that will downgrade the tp to the prior version but leave your firmware otherwise updated. I have not tried that yet but have read where others have done so with success.
see here:
http://forum.xda-developers.com/showthread.php?t=2048229
The pertinent info is quoted here, "READ CAREFULLY TO AVOID BRICKING YOUR DEVICE!
The latest full firmware (radio, etc.) is recommended. Check the firmware by pressing Menu while on your home screen, choose "Settings", "About" (bottom of list), "Software Information", "More". If your baseband is less than 1.12.11.1210, you have old firmware and should update else you could have problems with your data connection, reboots, etc. If you're s-off, you can flash the 3.16 firmware via one of the options here. Please do not use other firmware sources or you may brick your device! Note that both the full 3.16 firmware and the new touch panel firmware are recommended for best performance, but be aware that the new touch panel firmware will only work with 3.16 based ROMs! If you tend to switch between 3.15 and 3.16 ROMs or you like to try AOSP ROMs, stick with the old touch panel firmware and don't flash the touch panel update...."
There is a link in there you will find on the original that will eventually get you here:
[FIRMWARE][S-OFF] Jewel Firmware Collection - Latest: 3.16.651.3 OTA - theMikMik
I am thinking that the tp code (for downgrading purposes only) listed under the 3.15 firmware would fix you up. I think you need to flash it in bootloader, as well.
That is PROBABLY the right track for you, I have not done it myself, I still have the old tp version. Maybe try reading up in the last thread I linked to and confirm these observations for yourself before you flash anything.
Let us know what you come up with, please.
edit: So yes, on the new firmware, minus the TP update, my touchscreen does work with the Pacman rom. Only thing to really confirm would be if that file I pointed you to would actually work to downgrade your tp and the mode of install, flash vs bootloader.
Read, ask questions, don't brick your phone!
Reckon i will play with this, Ver.18 and inverted Gapps, now that i have it on here.