Yes alternators can have intermittent issues, but you have to answer a few questions first. How old is your battery? ( They only last 4-5 years ). Do you have the stock alternator in there? Have you looked at the wiring harness that connects to the alternator? Have you cleaned your battery terminals and coated them with purple protectant?
SOURCE: 1996 Jeep Grand Cherokee intermittent voltage drop, lose electric
I wont list this as a solution, but it seems that working in the area of the alt may have moved around some wiring...the alt may be OK but perhaps an adjacent wire (maybe a ground) is not well connected. Also check crimped on wire loops on alt connectors..they like to corrode at the crimp where it crushes on the actual wire.
SOURCE: 96 grand Cherokee charging problem
There is a 60A fuse in the power distribution box near the battery it is for your alt. Possibly there is a short or partially broken wire in the column harness. If shorted it may be causing fuse to blow, but that would need to be checked.
SOURCE: '97 jeep cherokee sport reads negative on battery
Have you checked the battery cable connections? If so, check the negative battery cable from the battery to the body and from the battery to the engine for breaks or if they are loose. If good, check the positive wire going to the starter, there is also an inline fuse in the pos. cable to the starter that might have blown. But, my guess is that the battery cables are loose. Hope that this helped, good luck. Let me know how it went. I'll be here if you still need me.
Bryon
SOURCE: 2001 Jeep wrangler not charging. Alternator has
on the field wires ones a posative and one a negative and the single post gets connected to a wire that runs straight to the main fuse box in the engine compartment then is fused to another wire that goes to the battery have that fuse checked it could be your problem as far as the feild wires the positive side only works when you start the vehicle up to engage the field
SOURCE: Grand Cherokee wont start, clicking coming from interior fuse box
Bare or burned wire, most likely battery cable or alternator cable near exhaust system which might be making contact with a metal part somewhere, off and on, because of bumps, vibration, etc.
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