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I just did my fusible links, or should I say put some in where they were supposed to be. You can reach down and take the large and small nuts off the starter solenoid without removing anything. If you don't have long arms like me you might crawl underneath and do it. If you really want to get the wires up close to you then you can take the connections loose from the alternator, but its not necessary.
When your truck is running you should have about 13.8 volts. If your voltake does not increase after the truck is running you have an alt problem or possibly a wiring issue.
Don't take this the wrong way; you are making this harder than it has to be. Just test voltage at the back of the alt and ground for 13.8 volts if you don't have it replace the alt. If you have 13.8 at there and not the battery then replace the wire from the alt to the starter with the fusible link installed inline. No need to wait until you pull the engine. Also you don't need to pull the engine to make repairs to the wire harness. I removed my entire wire harness to make the changes I wanted and reinstalled it when I was done. Its easy to just unplug untie and unbolt and pull it out. There is no better way to inspect it and know where you are really at than to lay it out on your workbench. If you really want to run a wire from the alt to the battery to see if it charges the battery per your gauge. Just hook up one half of a jumper cable and check the gauge.