I've got two kayaks, one closed cockpit sea kayak, necky looksha 14, and a Sit-on-top wilderness systems freedom 15. Both have sealed hatches, are comparable in weight, space and speed. Ive used them both on big water with no issues but the sit-on-top is relatively new to me. Wondering if your BWCA style tripping, anyone has a preference. I feel like I would like the SOT better.

I have a Necky Looksha 14 myself, and don't think it would be a real good candidate. Though the SOT may be harder to find a way of attaching a portage yoke. I've carried a SOT using a thigh strap as a sling, but it wasn't real comfortable. If you could find a way to portage it comfortably, the SOT would be preferable. Rec boats tend to be a bit better due to the ease of getting in/out and the ability to use a clamp-on yoke.

I'm working on a folding yoke design for the SOT. Ill post pics when I have a finished product, as long as it works of course.

That's great. I'd be interested in seeing them.

I'm debating drilling holes for a quick mounting system. It would be smaller holes and I figure I could seal them with O-rings, washers or whatever it takes to get a good seal. Can you think of a reason not to do this?

Nope, though I've not been the type to change the outfitting on my boats.

My thoughts on a quick attach yoke were to use the brackets for attaching stabilizer floats from spring creek.

Kinda like this only a yoke instead and at the center of gravity.

My sot has fairly large side rails so these would probably work for my situation. My kayak is banned in the bwca though so I would be using it somewhere else like timber-frear..

Bwca is tripping. A sot is fishing, ocean. I have a necky looks a IV 17 foot Kevlar. Two hatches and 45 lbs. Great tripping boat
I caarry it on my shouder