I am adding this how-to in case people need it, for return their device to Google, etc.
This is NOT meant to replace going through the steps in post #1. They are there for your learning, and should be used as a primary method of returning your device to stock. However, if your USB port is indeed messed up, then you will not be able to use the instructions in post #1.
Warning: if your USB port is indeed broken, and you complete all the steps below, you will have NO possible way at all to unlock your bootloader, or get root, or install a custom recovery. Period.
Note: I have not tested the zip in step 3 yet.
1) Ensure that you have root, and a custom recovery (CWM or TWRP) installed;
2) Download segv11's
BootUnlocker app from the Play Store, install it and lock your bootloader with it;
3) Download
this file (stock JOP40D ROM, kernel/ramdisk, radio and recovery) and place it on your device; EDIT: New file will be uploaded soon.
4) Reboot into CWM and flash the file you downloaded in step 3;
5) Turn off your device and reboot into the bootloader;
6) Go to recovery and access the stock recovery menu (i.e., when you see the android with the red triangle, hold power and press vol up) and do a factory reset and then wipe cache.
7) Done. Now you are fully stock JOP40D with a locked bootloader.