Got stranded today.
 

I'm pretty sure it's MS3 related. Had a quick errand to run. It's cold and rainy, so I had lights, heater and wipers going. I noticed the wipers only seemed to have 1 speed(real slow). Pulled in at my stepsons school and the idle was funny (oscillating between 1800-2200 rpm). Turned the car off, ran inside, came back out and the battery is to weak to start the car. Got a jump-start and headed home thinking I need a new battery. On the way home wipers seem to be working at normal speed now..hmm. Got home turned the car off and started it back up. It started up well with just 10 minutes of charge time. I turned it off and restarted it multiple times with everything turned on to try to strain the battery, but it handled it fine. I checked bat. voltage at @12-13 volts, started the car and checked again at @13-14 volts. I'm thinking there's either a sporadic grounding issue somewhere or a problem with the alternator control. Any idea's?

Check your alternator hot wire and your battery terminals

Alternator hot wire and both battery terminals are tight.

I have checked every connection. I checked both bat. terminals, the 2 ecu connectors hooked to the ecu, the large wire at the alternator and the flat plug at the alternator. I don't trust the car now and I don't know what else to check. I am really thinking it may be the alt. control circuit in the MS3.

do you have any squeals or squeaks from the belt?

Nope, the belt is nice and tight.

Check grounds.

All of the above

Do you still have the stock ecu? Maybe you could plug it in just to see if the car starts.

Problem popped back up, luckily I was at the house. I started the car and it idled for about 5 minutes while I was doing something else. I got back in it and flipped on the wipers and noticed them going very slowly. I jumped out, popped the trunk and checked the battery with a multimeter. It was showing 10 volts. I turned the key off and turned it back on and the battery showed 13 volts, but didn't have enough juice left to start the car. I hooked my jumper box up, fired the car up, unhhoked the jumper box and rechecked the battery agian and it was showing just over 13 volts. I've checked the grounds, the alternator plugs, and battery terminals. I had the battery light enabled on my MS3 but it never came on, I havent checked to see what my lower limit is set to yet though. Any idea's?

I ended up running a NA8 alternator on my 99 after having similar intermittent voltage issues that I couldn't figure out. If you can't figure out the problem, that's one way to avoid it all together.

That's what I'm leaning towards. It sounds like a bit of a hassle to convert, but it has to be better than this.

You are in Ohio? I would start by blaming your battery, I would imagine its pretty cold out there right now. Pull the battery and charge it overnight somewhere that isn't 34° ambient? Start with a good solid charge and see where that takes you.