I can confirm that the method OMJ posted works. I used it for my E3D a few days ago and my brother's just yesterday.
The issue where you're stuck at the HTC boot screen is due to S-On status of the hboot 1.5 root method. It sticks (I think) because the Rom flashes but the kernel doesn't.
Another method to flash is with the Flash Image GUI app below. I used this to go from v. 3.0 to v. 3.1. The app basically flashes the kernel first then allows you to (wipe caches if you choose) reboot to recovery and flash the rest of the Rom as usual. This method is very convenient and user friendly.
I'd assume as long as your on a rooted Rom with a 2.17 firmware base (like the previous pre-ICS OMJ roms) you should be fine to just flash the new OMJ v.3.1 Rom using this method. Not sure where a super wipe fits in this equation or if it'd be necessary but if you're really worried I guess you could superwipe after successfully flashing v.3.1 and then reflash it again...? (OMJ pipe in here if I'm off base lol).
Flash GUI link with explanation from xda:
http://forum.xda-developers.com/show....php?t=1453617
Also available in the Play Store not sure if there's a difference in the versions but this one is $0.99:
https://play.google.com/store/apps/d...imagegui&hl=en
Hope this helps so my accidental journey into hboot 1.5-land wouldn't have been in veign lol
Positive Vibrations