[HTC EVO 3D] caderyn19:
I didn't unplug mine and it worked fine. I was VERY confused at first, but then I realized that holding Vol+, Vol-, and Pwr will reset the phone. Don't unplug it, and when it says to hold those buttons, HOLD THEM until the phone reboots. It reboots on its own, but it wants you to reboot it on top of its reboot. You will hear your PC connect and disconnect, as well as seeing ADB pull and push a couple things.

Edit the batch file and take out the "echo off" in the first line and you will get to see all the nitty gritty going on. That was a big help, because I like to know what's going on.

What it is doing is looking for the quickly-timed vulnerability in the unrooted boot process. Once it hits that point the batch file knows and runs it's first two commands.

But seriously, don't unplug it.. just follow what the batch file says to do and it will go through. Once it says "you haz root" adb pull /data /boot and /system partitions respectively (will take time). Also, get Titanium Backup before the rooting process (iceman is correct. You can download root programs, they just won't work without root), just in case you can't access the network, though you should be able to (and there's no WiFi, which you know). I sent a few text messages while I was waiting for the backup, but I heeded the warnings and didn't touch the status bar. My phone didn't make noise or vibrate so I knew it was very iffy to push it to do anything. Run Titanium backup and backup everything. Run unroot.bat to clean up your fiddling around. Run the HTC Unlock. Bye bye data, but not for real!

Once that's done, go back into bootloader>Fastboot USB and you can use the "fastboot flash boot recovery.img". Once you have your custom recovery flashed, you're set.

But, first thing is always first. Hold Vol- and power to go into bootloader (from powered down state, fastboot in "Power" disabled... Just leave it disabled forever...) Go into fastboot and select recovery. In there you most likely will have an option to backup your NAND. Do it. Full backup.

Next, once you have picked a ROM (custom or stock kernel), copy it to your computer (or download it to PC and transfer to SD card, leaving a copy on both). Open the ROM with WinRAR or other zip program and extract the kernel.

Reboot into bootloader (TWRP has a reboot menu) and select recovery. This should bring you to your recovery menu. You will have an option to flash/install a zip file. Go in there and find your ROM. (You might have to clear delvik, etc. Look on the ROM page for installation instructions, but the jist of it is right here.) Let it install, and then go back to the main menu. Reboot to bootloader and go into fastboot.

This part requires you to have added a couple adb tools to your "Environment variables" so you can use the adb commands globally... Head to the Google SDK site to find the right paths, I don't remember them off the top of my head.

On your PC, open a command prompt window and navigate to where you extracted the kernel. Do a "dir" to make sure you see boot.img, not the folder boot.img is in. Type (while in Fastboot USB) "fastboot flash boot boot.img" (no quotes in DOS... I call it DOS... But no quotes) and it will flash the custom kernel.

The reason for manually flashing the kernel is because (as stated previously) S-On doesn't let us access the /boot partition anywhere else BUT the bootloader/fastboot when unlocked. So when your ROM flashing process said "flashing kernel", it lied. It can't. Hope this helps!