Electrical issue with alternator?
 

Hey all
Need some advice...again. Try to follow me on this, it might get convoluted. I've got a 1000 watt stereo system in my '96 ZJ. I have a 1 farad capacitor for the subs and amps. About a month or so ago, I noticed that the battery gauge needle started to dip below the normal 13.5-14 volt level. Even while I'm driving, I'll notice the needle fluctuating. The battery is barely 1 month old and the alternator is just over a year old. I bought it from Autozone, I think it was a re-manufactured one. The last few times I drove, I drove without the stereo playing with the idea that the alternator will charge the battery better. Well, today I went to Autozone to price some other stuff and checked the display on the capacitor while it was running...it should read 14.1-14.4 with the engine running. Today it read 13.6-13.7. I was thinking and it was suggested that I put a 120 amp alternator in in place of the stock 90 amp. The 120 amp from a V8 Jeep will fit but someone mentioned that it will send a funky signal to the pcm and it could cause me problems. Any idea's or input on this would be much appreciated.
Thanks.

your computer controls the amount of chargeing not the alt a bigger alt sholud not affect the ecm if theres a bigger amp alt sold for it it will work

As long as you're above 13.5 volts you'll be fine. If you're reading this voltage at the cap in the back of the Jeep, you have to figure in a slight voltage drop between the battary and cap. Your charging system is doing very well.