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Electrical Tech / charging issues, new alt and battery
So I have a 1989 cougar ls (3.8L V6) with 41,000 original miles on it. For various reasons unrelated to this post, I have had to take apart most of my dash (including my radio, HVAC controls/wiring, and various small interior components). Consequently, my glaring lack of technical skill/excessive faffing about with wires caused me to short circuit something. Oops. Also during this escapade of mine, my alternator decided to out (whether or not my tinkering caused the failure i may never know), taking my battery with it. And so I swallowed hard and spent many, many money out of my measly salary to replace them. However, despite my brand new alternator putting out its expected voltage (about 13.7 I think), that voltage is not making it back to my battery to recharge it. F**k. I have started checking for power drains (shorted out wires, things left on, errant pigtails touching the frame, etc.) and I am finding none. Next, I went after my fuse box with a fuse puller and removed anything that was not strictly necessary (like interior lights and my a/c). This still didn't solve my escaping voltage problem. I talked with various car guys that i know, and they suggested I check the fusible link protecting my ignition and/or charging systems. Trouble is, I can't find the things. The repair guide states that they are located "near the starter relay." The guide also says that the fusible links for the ignition feed and charging systems are 16 GA (Black) and 14 GA (dark green), respectively. Can anyone help me out with where they might be hiding? Any advice would be appreciated.
UPDATE: I have taken the alternator in for testing, and it is definitely working. I have also replaced the connector on the alternator. I checked/replaced all fusible links and put new terminals on the battery wires (to improve the connections to the battery posts). My battery is still leaking voltage. I wired my multimeter to my battery and then ran wires up to my dash in order to get real time data on my battery voltage. It's still leaking. I was informed by the guy at the auto parts store that my battery is slightly too small for my car. Could this be causing my problem?