I see it's been a couple of years on this, but my 99 Grand Cherokee seems to be doing some similar things and I was wondering if you ever found the cause.
1) Driver's window on auto-down, goes for a bit then stops and have to hit it a few times to get it going again.
2) haven't noticed the lights going on at night, but battery drains completely if left sitting for more than one day
3) passenger-side brake light does not work when lights are on, however, does work when lights are off, but when lights are off the driver side brake light does not work, but works when the lights are on.
It also likes to stall randomly and throw a code for the crank sensor and the blower motor has failed repeatedly
have taken it in for an electrical diagnosis and and was told that the blower shouldn't be used until it's replaced... so not helpful.