Usually, you're compeletely overpowered when you reach JC.
Here, I think your best bet was to shoot him with your hyperblaster, and use some BFG shots to clear barons if the screen started filling too much.
Btw, high power BFG is a pure waste. keep bulks to increase the number of shots (1 more shot per bulk, B3 BFG has 220 cells !).
You might also have sacrificed your intuition to the envirosuit, for the resistances against both barons and rockets.
For fight in the open, the best is to have an insane firepower. For me, most usuful skill are, in that order : SoB, EE, Fin. MCe helps a lot too, especially if you got enough speed to stay out of LOS of your opponents, but I'm not sure hit&run works for JC (I never tried it).
Without enough firepower, you'll quickly get swarmed, and need to get back to some cover... which hell fortress doesn't offer.