[Motorola Atrix HD] gzrecoil:
Edit: There seems to have been a utility created to automate most of this process. I have not tried, check it out.

http://xdaforums.com/showthread.php?t=1985031

Hey guys, took me quite a bit of time perusing the cheesecake thread to figure this out, so I figured I would do my best to put all the info in one post.

First, you want to flash back to stock ICS. I had apps frozen etc. and was getting errors installing jellybean, so do this first.

Step 1: Download & install Motorola drivers - https://motorola-global-portal.custhelp.com/app/answers/detail/a_id/88481/~/drivers

Edit: Steps 2-8 might be able to be shipped if you are on stock ICS, but if you get an error flashing Jellybean, try to reflash.

Step 2: Download & install RSD lite 6.14(Users noting newer versions not working) http://www.mediafire.com/?yw9dh89jtqii71e

Step 3: Download Latest stock ICS: http://sbf.droid-developers.org/dinara/7.7.1Q-144_MB886_MR1-22_SIGNED_CFC.xml.zip (Thanks Huatz84)

Step 4: Download Edited XML file:https://www.box.com/s/oo8vcdv7lkyf6n51el6i (Thanks Huatz84)

Step 5: Extract .zip file, and overwrite the XML file with the one downloaded above.

Step 6: Launch RSD lite and select the modified XML file located within the folder you extracted

Step 7: Turn off phone, and boot into bootloader mode by holding power button + volume down

Step 8: Start flashing ICS through RSD lite

Step 9: Reobtain root using motofail2go (http://xdaforums.com/showthread.php?goto=newpost&t=1940594)

Step 10: Retain root: http://xdaforums.com/showpost.php?p=33323701&postcount=65 (Thanks Marykzz)

while on ics, 1. root, 2. use ota to backup, 3.temp unroot, 4. restore root

1.) Update the superuser app in the play store.

2.) Update the binaries in the super user app itself..

Edit: Neroga's post about retaining root is easier to follow.

Root on ICS, UPDATE superuser and replace the apk in /system/app with the one in /data/app then reboot. Go into superuser and update the binary. Then use voodoo to back up root, temp unroot, then restore root and temp unroot, again. THEN flash the jellybean update, reinstall voodoo, and restore root. Worked on the first try for me.

If you did any modifications like google now or the 4.2 keyboard and camera, or removed any bloatware, then edit the modified xml and add back the line for wiping system when going back to stock ICS or you'll get errors when applying the jellybean update. Thanks Neroga!

Step 11: Download JellyBean 4.1 leak and save to SD card - http://www.sendspace.com/file/etujfp (Thanks Huatz84)

Step 12: Boot phone into recovery by holding power + volume up. Once you see the dead android guy, click both volume buttons at the same time.

Step 13: Apply update from SD card, select the Blur_Version.77.12.22.MB886.ATT.en.US.zip which is 4.1 leak, and apply the update.

Step 14: Restore root

If I am missing anything, please let me know in comments, and I will modify my original post. This is the best I could do to get everything in one place for those looking to make the jump. I had to factory reset a few times after installing 4.1 due to a setup error, and my screen turning off during phone calls, and lost root. A lot of people were able to keep it though.

Jellybean is working great for me, everything is much more fluid, and I really like the quick settings when you scroll left from the home screen.

Good luck, and happy flashing! Reference cheesecake thread for anything I missed or ask in comments, there is a lot of reading in cheesecake thread.