The alt. voltage needs to be around 1V higher than that of the battery (12.6 fully charged). See you need to isolate each system and then attack the system with the problem. And you cant just measure the resistance in a ciricuit and expect it to work like expected. You see the DMM outputs a small voltage though the leads and then measures the voltage in the circuit at the other end (or amperage I cant remember at this time). So if there is just the slightest of a good path the resistance will be low. The best test is a voltage drop. This way you can actually know how much voltage its at each point in the circuit and it is far easier to determine the point at which there is a high resistance due to corrosion or some such. I have a fluke 87 as well its a very powerfull tool, but only to those who know how to use it properly.

So check the voltage at key points in the system, starter, alt, fuse blocks, ect. with the key off you should get 12.6V or so ± a few tenths depending on the circuit. If you find a big drop in voltage you will know where the problem is. Check the grounds if you find voltage on a ground then there is a problem with a connection somewhere.

I would also isolate the entire battery and first see what the bat voltage is.

Then put it back in and connect it (make sure it is fully charged). If you find a large drop in voltage once it is connected then start pulling fuses and or relays one at a time until you see the voltage go back up.

Hope this helps if not find out the items I mentioned and report back.