I was in a similar situation. Pardon my ignorance but I am very new to this. This was my situation and what I did.
My phone is rooted and I have ROM Manager installed and flashed CWM. I previously flashed Gingersteem Extreme (Modded, Themed, and Custom kernel) from PlayfulGod. When I did, there were certain things that did not work correctly (apps were not showing up on Play Store) so I backed it up and flashed GSE-C v1.0 from PlayfulGod and it worked GREAT. It wasn't nearly as cool, but it functioned perfectly.
A few days later I decided to change my boot animation to the R2D2 boot animation. I then rebooted my phone and was stuck in an infinite loop. I tried pulling the battery, and rebooting my phone several times. I also let it loop for about 10 min. I did notice that I could hit the power/lock button and my screen would shut off and on which was wierd...anyways
I decided to try a hard reset (turn the phone off then hold power, vol. up/vol. down until it vibrates then releasing the power button).
Once prompted, I hit the power button to reset and then again to confirm. It then launched CWM.
I scrolled down to backup and restore using the vol. down and selected it with the power button.
I scrolled down to restore and selected the first Gingersteem Extreme backup I did.
It did its thing and I then told it to continue with the reboot and poof...it was fixed.
I don't know if it was because of the custom boot animation on that particular ROM but I just wanted to put this out there for anyone who is in the same situation I was.
By the way. Once I restored the Gingersteem Extreme (Modded, Themed, and Custom kernel) from PlayfulGod it worked perfect. All of the bugs were gone. Props to PlayfulGod on this one. Keep them coming.