Try the battery before you try the alternator. Sometimes a battery can be so dead that it forces the alternator to work harder, causing pulsations in the lights, and guages. So a bad battery can make it look like your alternator is jacked. Then check the alternator.
I know that this is exactly what you don't want to hear, but I have the exact same problem. Car runs good at startup, then almost stalls before recovering-- at which point the pulsing begins. It isn't just the electronics, but the engine too. It pulses forward then back, like i get on the gas, then let off, then back on again. I took it in to a trusted dealer, hoping to God that it was the battery, or even the alternator.
Unfortunately, it was my harness itself. Quote? $2500 parts and labor. Problem now is, who has them. I have been seeing quotes around $1200 for the harness itself, but I am currently looking for something less expensive.
As for now, try the battery, then the alternator, then look into the harness. Let's hope it isn't the harness!