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UPDATE: 01/15
I did the "pull of the negative" alternator test and once I took off the negative, my car died
Another question: the wire connected unto the bold that has the rubber covering, is that a ground or is that the power? Within the last day I've heard it was the ground...while some say its the power. So which is it?
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while you did fix your problem, it's good to know a few more things about troubleshooting the charging system. for others that may have a similar problem, too:
first off, you shouldn't really be doing the 'negative wire' test. it worked on older cars without fancy computer electronics. but today's (and yesterday's) cars use the battery as sort of a voltage sink so voltage and even current spikes are absorbed by the battery and thus are not transferd to the electronics. that could easily kill any number of your ECM components. and two, it tells you nothing. the car still dies, but how?
with a voltmeter, you can get a bit more technical. as mentioned, you are looking for 13.5-14.5 volts with ALL the loads on, across the battery. anything less, and you want to see what the voltage is directly at the alternator output terminal (the one with the rubber cap. the alternator grounds through the case, and the rubber cover keeps the output from shorting to ground). if the voltage is like normal, bam! your problem is in the wiring between the battery and the alternator. if the voltage is still low, you need to take the new alternator out and have it bench tested. btw, did the parts store test your old alternator? they should, otherwise they waste your time, and theirs.
other things: make sure your cable clamps are CLEAN at the battery, and TIGHT. make sure your output terminal wire is tight on the stud, and clean. make sure the ground wire is in good condition. normal car batteries can't handle many deep cycles (use until it's completely drained then charged back up). and alternators aren't meant to charge a completely discharged battery, only to keep it topped off. try to charge a completely discharged battery with an alternator can kill it quick.
check your fuses. taking the negative off while the engine is running could have popped one. and check your amp. the power supply inside could be stuck on, creating a drain. check your alarm, it could be draining more than normal also. with the engine off, take the negative cable off and put an ammeter in series between the battery and the cable. if you get more than 1/2 amp or so (some may argue a smaller number, which may be correct) you have a drain and have to hunt it down.
don't be throwing parts at it. try to find the root cause. unplugging all aftermarket do-dads can help narrow down the hunt, too.