NP:
Welcome!
You'll probably notice that most folks here use their real names; it's one of the things that help to make this forum great!

I'm seriously considering a CLC Creature Comfort Seat or a Redfish seat, anyone else have any other aftermarket seat recommendations for wood kayaks?

I've used the 'Happy Bottom' (aka Creature Comfort) seat and it was OK - it was one of the options that Mariner Kayaks in Seattle offered; my wife's Elan came with one. I much prefer seats that are 'slippery' as it's easier to get good rotation for an efficient stroke. The Redfish seats are popular, and I think they come pre-fitted for some Pygmy designs.

I've seen several videos on how to make your own out of minicell foam, but the convex carbide carving discs they use are $70 ea.........

You can grind foam with a 36 grit disk in a 5" grinder, but it's tricky. You can also shape foam by hand with rasps and 'DragonSkin' metal abrasive.

As for the toggle handles, the guy I bought the Borealis from didn't install any

End toggles are important for safety as well as boat moving; a lot of my paddling friends always carry the boat by the hull (not the toggles) but they have good toggles for on-water safety.
My guess is that the builder didn't install perimeter deck lines either ?? You should install those as well.

The builder of my boat suggested drilling the hull for 1/2" dowel rod (he recommended oak), epoxying that in place, cut the dowel off flush with the hull, then drill out the center of the dowel and feed the line attaching the toggle handle.

I doubt that the builder had actually done that before. I don't think that would be a very waterproof or rot-proof solution, and a 1/2" dowel won't leave enough wall thickness to accommodate even 3/16" line. If you do choose this method, drill the wood before you glue it in place. I've used a plastic (grey PVC) tube roughened and epoxied in place, in some canoes. Or you can do an epoxy end pour and just drill through that; it's a much more reliably waterproof method.
Single-line toggles are much safer than 'strap' or 'rope loop' handles. You can buy the actual rubber handles cheaply on eBay or drill a piece of PVC conduit.