Rear Disc/ MC problems

i just finished up the grand cherokee rear disc swap on my xj. had some issues with the rear pads being way too tight on the caliper brackets and messed one of them up trying to get it in. i think i'm going to grind some of the metal tomorrow because as of right now, the pads cannot move side to side, they are very tight in the brackets. anyways, the bigger issue is that when i went to add brake fluid before bleeding the rear (i put in new hard lines too) the resevoir was bone dry:scared: both ports were exposed. the brake light came on but i think it was just because there was no pressure in the rear lines. when i finished bleeding the rears, the light went out. my jeep stops better than it did and the pedal has a decent feel but everything i have read about bleeding brakes says make sure you don't let the resevoir run dry! but i never read why. is it really screwed up or is there just air in the system that needs to be bled out?
Thanks!

Letting it go bone dry puts alot of air in the tubes. If you do a good bleed job you should be fine. I don't know the exact reason why your not supposed to, but I did it to mine and just had to spend alot more time bleeding it. I bled it once, waited for a few hours, bled it again (found some air). Then I did it again the next morning. The brakes have been fine since.

bleed bleed and bleed till you cant bleed no more. Then.... you should be fine. Make sure you bleed the fronts too and the prop valve.

is there a regular nipple somewhere near where the hardlines connect to bleed the prop valve?
Thanks

Bleed it in the very front IIRC