battery or altenator issue
A new alternator is the way you want to go if cleaning doesn't help and a new one costs $105.00 shipped and is a 130amp vs. the stock 105amp. You could install it in an afternoon with a buddy or by yourself.
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as well on mine during removal. if your good with soldering its fixable, i just piled solder into the hole in the connector and took another wire and soldered the whole thing back together. i believe the wire is for your gauge, if you cant get it on, no big deal. trust me just replace the alternator, mine was like $130 for a new one, and it took me 45min even with the wire braking. and im only 17 haha. hope this helps, like i said i did this last night so i know what your going through. pm me for anything else
to emissions. just get a dyno-tune, you should be able to pass emissions after that. in IL i dont think there is a visual inspection. 
