I think I'll add my experience, just to add something to common knowledge.
Yesterday I flashed paranoid android (root was obtained via towel root and recovery installed through autorec. No problem there, backed up my rooted stock rom). My attempts:
1) flashed pa 4.6 beta 5 20141023 (obtained through pa website), followed by pa mini modular gapps. Booted all right, but no signal, so I restored my backup. Stock rom still booting all right.....
Same journey as you, installed latest PA beta, lost IMEI, no call service so restored a backup of CloudyG3 2.0. That was last night. I don't recall seeing a black line untill 10min ago when i played a game for 5-10m and then got back to desktop. Maybe it was there before, though i tend to notice such things. Anyway running the fix app, let's see what it does. Amazes me it doesn't bother me so much, but had it been a new phone like many of you, i think it would very much. Be strong, hang in there