90 inline 6 will start but not idle

Battery needs to have a good /full charge on it. Try keeping the engine at a higher idle when removing jumper cables and see if it stays running with your foot on the gas. If so, battery may be the culprit.

You have rvc/regulated voltage control, that circuitry is in your pcm. I'm not saying the pcm is faulty, at the moment, I don't know? You also have a battery temp sensor in the battery tray housing, that might cause problems?
Check for applicable charging system trouble codes, if you haven't already.

Something mechanical, ignition, or fuel.
It can run rough under a load such as in gear and ok in neutral with no load. Have you checked the plugs and dist cap ?

the cable /fuse to alternator has nothing to do with the start and run function if the battery is charged up and in good condition ,sounds like the main battery cables have a bad contact/connection or battery is shot<follow battery cables and remove all points of connection in engine bay area clean contacts with sandpaper and resecure all connections 1 AT A TIME! to make sure none are swapped around by mistake ) on both earth cable/negative and the positive/power cables,make sure terminals on battery are clean and tight , try boosting/jump starting your battery with jumper cables connected from another cars battery positive to positive .........negative to negative and see if it starts ,i doubt the problem of starting up is the alternator unless battery is flat and not being charged by alternator ,by jump starting with another baterry will give you the answer once all baterry cables and connections are clean and secure

Check battery cables are correct ! Prime suspect here ! Alternator may be damaged and shorting .. Don't drive any car that will melt jumper cables ! Something very basic wrong here.

I think the seal under the cap is bad. Try replacing it with a new cap. Overtime these will not hold pressure, causing fluid to flow out. Sometimes it will run hot, other times it will be fine.

have the throttle position sensor checked for correct voltage

Replace all fuses. Have battery and alternator checked for free at an auto store. Then use a code reader to determine if any new codes are showing up from the improper jump.

Possible, But it should idle with the jumper cable hooked up. after charging the battery, does it start on its own?

Well it could be many things, But have you relpaced the dist. cap and rotor, within the last 15,000 miles or wires and plugs??? next step is the coil ? then it gets fun. like timing. but I think most jeeps with a Inline 6 have a bullet proof engine for the most part. As we all know there is plenty of semi's on the road. well the same set up is there. as an Inline Jeep. I would have to say 90% of semi's on the road are inline 6 cyl. engines. and may of them go to 1million miles.
so plugs,wires, cap, rotor and ignition coil. that is a good starting point.