Check Engine Light

I have had my 97 Cobra for a little over a week. It has 104k on it. It was a little chilly yesterday morning and raining. I started the car and it seemed to idle a little high 1100 (usually at 800). I figured it was because of the weather and needed to warm up a bit.

By the time I got out of my apartment complex it was idling normal but still seemed a little rough and bogged down. I got about 3 miles up the road then my check engine light came on. The exhaust sounds totally different then what it normally sounds like. Its more raspy and at an idle it kinda sounds like it's sputtering. (Hard to describe)

From those symptoms does anyone have a clue where I should start looking?

Mods are 373 gears, bbk x pipe, and flowmaster 40 series.

Thanks for any help!

(Also posted on stvperformance.com)

I stopped by Autozone and had them do a check for me.

It said Misfire in cyl 3. Okay, I just got the car not too long ago, wire and plugs were coming this weekend. Not a big deal. I thank the lady and get in my car to leave. It won't start. The starter just clicks and clicks.

The battery is reading 8. It has no charge. So, we jump the car and hook it up again to see if it's being charged. Nope, it isn't, the car dies.

So I'm thinking the misfire was because of not enough power to the plugs therefor the bogging down and all is because of this. The battery is a red top optima so it's being trickle charged now and I'll go take the car home once it's done.

Hopefully it's the alternator and not wiring.

Does this sound logical at all?