Alternator Gremlins

[Sparky]

What year and type of vehicle do you have? This would help us better point you in a direction.
From what you have posted, it sounds like a couple things could be at fault.

As Jake mentioned, checking the wiring and output at the Alternator is a good start. You would need a Digital Voltmeter, (DVOM) like a Fluke 83 or 87. Set the meter to DC Voltage, with the vehicle running at an idle, check the output at the back of the alternator and at the battery. Like Jake said, you should be around 13 .8 at the Battery and about the same at the Alternator.
Increasing engine speed should make the voltage go up to around 14.5 volts.

You should also check the Voltage Regulator, make sure the connections are clean.

There is a full test procedure on how to check the Voltage Regulator here,
http://www.users.bigpond.com/jack_st...to_elec_2.html
One of the easiest test, is to Jump Terminlals B (Battery, Red wire) & F (Field, Blue wire) at an idle.
If the the Alternator voltage goes up, then you possibly have a bad Regulator.
But you should run through the other test first and make sure you have the proper signals on the other wires.

The big wires at the horn relay are actually a junction point, for the inside car power. One of them should be Battery Power and the other runs into the car, to the Fuse Box. Check these and make sure they're not corroded, broken, etc.

The other nice advancemnt to come about is a one wire alternator. You can get these from Power Master http://www.powermastermotorsports.com/
and East Coast electric http://www.ecae.com/
A one wire alternator can make life a lot simpler with the charging system. One wire form the alternator to the battery and that's it.

On another note, reading through your post with all the accessories you have on the car, you may want to consider something over a 100 amps.

I hope this helps,
Sparky