The culprit was the brushes and slip ring worn out to the point that physical connection was lost intermittently.
IMPORTANT NOTE if you have a 2000 Wrangler:
It is the only year to have an externally regulated alternator and alternator is unique for that year only and is quite rare. The voltage regulator is in the ECM(obviously a very stupid idea)
Mods: Please edit title to reflect issue being year specific as this may be helpfull in search function.