Probably something to do with the radiator. Maybe clogged? Clogged hoses or something. If the coolant is boiling, it's obviously getting too hot. Is your fan kicking on when it needs to? There a ton of reasons it could be cooing improperly.
Try flushing the system, and see if you get some nasty crap in your old coolant.
2000 TJ - JB Headers FM Super 44. RC 3.25'' on 31s.