[:@]Have a 2001 Civic Ex. On the way home from work. headlights began getting dimmer,battery light came on, gauges went funky. It would start acting normal then revert back to funkyness. Took it to a garage they dida diagnostic and said the alternator was not charging, which I already suspected. They found burned wire and broken wire in the alternator harness. Replaced with new one, same problem, then they decided to replace the alternator. After all the money, car is still the same[:@]!! I paid for repairs to nowhere! Help!

 

There are likely additional shorted wires in the alternator circuit that have not yet been discovered.

 

[&o]Mistake, they replaced regulator harness.

 

If there were shorted wires, wouldn't it blow fuses? How about ground circuits?

 

The fact that you already found burned, shorted wires to the voltage regulator in the alternator together with the odd behavior of the gauges leads me to suspect that you have an undiscovered short somewhere else in the alternator circuit (see picture). Carefully trace and inspect the wires and harnesses running to and from the alternator.