could be the regulator ive had the problem before, so now im running a 270amp dc power alternator internally regulated, hopefully this helps.
go to autozone and get a load test on your alt you do not have to take it off to get it tested just take your car there, seems like you have another dead alt
are you running anything extra like subs amps and other after market stuff that draws amps?
my amp killed my stock alt my amp needs 500 amps of current to run, and the alt is only a 160 or so stock IIRC, so the alt trying to charge 4 batteries and still run all of the stock things like lights,gauges, ect etc adds up and you end up with a dead alt
here is the part this is a stock 99 navigator alt too