If you upgrade your alternator - particularly beyond the stock 63amp (and it's questionable then) you really need to change how the wiring system works.
You'll need to buy a Voltmeter and install it under the dash or somewhere. You're going to make your ammeter useless.
The stock setup has all of the alt output going through the "bulkhead" connector and to the ammeter, then back out to the rest of the truck. With stock alternators, I've seen this connector melt/burn!
What you'll need to do is run a heavy gauge wire from the alt output directly to the battery post. This will divert all of the "charging" of the alternator back to the battery, and bypass the weak-link in the firewall.
Of course, your ammeter will show a discharge most of the time with this setup, but that's OK. Just keep an eye on the voltmeter instead.
Ideally, I'd switch to a Ford starter solenoid on the firewall (I had a hot-start problem anyhow). You can then run some battery cables from the alternator output right to the Ford solenoid (which in turn goes back to the battery directly). This is the easiest way.
You can then built an auxiliar fuse panel on the firewall. Maybe even two.
Wire one up directly to the Ford solenoid to get it's juice. On the other, you might hook up a 30amp (or a couple if you really need that much juice) relay between the aux fuse panel and the Ford solenoid/battery terminal. Energize this relay with a "keyed on" lead from the ignition system.
That way you can run "always hot" wires from the "always hot" fuse panel (maybe you want your KCs to be "on" even if the truck isn't running) - bypassing the weak factory wiring harness in the cab.
Use the "keyed on" aux fuse panel to wire up the rest of your stuff that should only be on when the key is ON or ACC - like a stereo amplifier, CB radio perhaps, maybe your foglights or KCs, etc.
-Tom Mandera, Helena MT
(I wrote a "wiring FAQ" some time ago that has some useful info for wiring aux stuff)