OK, first, what exact model of 980 Ti are you working on? I assume the reference board? This does matter, since each board design is obviously different, and each one is subject to its own unique modes of failure.Glad to have written here before! Sure thing, looking forward hearing from you!
Anyway, the 3ish ohms you're measuring on the 6 pin connector are mostly like the DC resistance of the GPU core. You can confirm this by checking for resistance between the 6 pin connector's positive pins (those furthest from the latch) and the positive terminal on one of the big capacitors in the core VRM. On a reference board, C247 is probably a good one to use - that's the uppermost. Positive is the side with the stripe.
What I suspect you'll find is that you have almost zero resistance between the connector and the positive side of that cap. What this means is that you have a short from the 12V input directly to the core VRM output. The most likely cause for this is that one of the high side FETs melted in one or more of the power stages. You'll need to figure out which power stages are connected to the 6 pin connector (I think it's the top four), and then determine which one of them is shorted. There are a few ways to go about this; the easiest is probably to inject 1V into the 12V power plane, and look for which one gets hot (using isopropanol or freeze spray as a bellweather if you need to). Failing that, you could just start removing them until the short goes away. The downside to this approach is that they're a pain in the ass to solder back on, and you will almost certainly damage them when you get them hot enough to remove, so you'll need at least four new ones, which may be difficult to find. Use a preheater to get the board up to 150C or so before you hit them with the hot air wand. That will help immensely.