What all (electrically) do you have turned on when you come to a stop and the headlamps go dim? With a 100A alternator, you're probably getting 40A or so at idle - if you're drawing too much at idle; the alternator can't keep up (until you speed up again,) the battery has to fill in the gap, and system voltage and current will both drop.
My 160A alternator (built for me) puts out about 90A at idle - which is still too much to run everything I've got! I mainly have the high-output alternators because I tend to give a lot of jump starts, and it saves wear on the battery. Given that I don't push the unit anywhere near as hard as it's designed to go, it is highly unlikely to wear out - with the Red Top, I don't touch much of the reserve capacity anyhow.
You might want to look into what electrical loads you're putting on the system at idle - I think the engine wants 10-15A to run (although I'm not sure,) the stereo may be a big drain, and if you've got a batch of lights, that's certainly going to cause you difficulty.
You're on the right track with the heavy mains leads and the ground updates (I've done much the same thing, using slightly smaller cable - 1AWG,) but if you've not got quite a lot of source, then the drains might be too much.
It should be borne in mind that smaller pullys on the alternator, on a daily driver, are quite likely to wear out the bearings in the unit rather quickly - because you're turning the rotor faster. I'm actually running about a 10% underdrive on my alternator - which is going to help because I'm turning the rotor slower than normal... I'd suggest the use of an overdrive (smaller) pully with a show car, or something that isn't driven often - but I like to use underdrive (larger) pullys on daily drivers. (I've got four in service, all high-output, all with 10% underdrive...)
5-90
