I'd always reccomend using the PMS board just because it's so good. They should be back in the store this week as Gman just finished assembling another batch. In regards to your ground question for regs like PTHs, you're good to just daisy chain all the ground connections on the regs together. Resistance through the wire doesn't make any sort of impact in scenarios like this, so long as your wires aren't stupidly long.
As for using the extra pins on the AV port, if you completely desolder the port from the Wii motherboard, you can use any of the pins that you want, except for ground. I don't think there are technically any "unused" pins, but there aren't any sort of internal resistors attached to the port, so every extra pin could hypothetically still be used. That sounds like a pretty neat idea for a breakout box, you'd just need to be careful that nobody potentially plugs in a cable that could connect things that shouldn't be connected...
When soldering to battery cells, you don't need any special equipment so long as your careful. It's best to rough up the contacts with sandpaper, and then quickly solder to the cells on a high heat setting. I generally use around 300C. This works fine for me on 18650s.
And no, it's not too late to set up VGA patches. Did you ever set your Wii to 480p in the Wii system menu before trimming? If not, you can still do that, it just takes a bit more effort on a trimmed Wii. From there, you can follow the rest of the steps exactly the same without any issues.