6ga./50amp breaker will be fine, and that TM should do "ok" for positioning and moving around in "toon'able" conditions. No sense in maxing out the TM since no matter how much thrust you have you still won't be fishing ENJOYABLY in a toon during a windstorm.
If you're dead set on using anchormates then a grapple anchor is out of the question, your stuck with mushroom or tri-fluted designs.... without chains. Neither are gonna hold very well in wind or boat wakes unless you let out enough line so they can dig in good, and sadly most anchormates don't hold enough line to do that in water deeper than 8-10ft. If that's good enough for your intended use then your in good shape.
You won't want to paint the rails cuz they'll just look like hell after a few outings, but the panels can be dressed up real nice with any automotive or marine spray paint and maybe some decal highlights/trim. As always the quality of the finish is in the surface prep. Keep the paint as thin as possible on any surface that is prone to flex.
Lots of ideas for livewells but before I go any further I'm gonna piss in your cheerios just a bit.
I wouldn't dump too much time/money/effort into anything that's gonna be supported by the pill shaped Tracker buggy toons with welded braces.....they just don't hold up well compared to "U" shaped toons on Lowe, Landau, SC, type toons, which are what I specifically look for when restoring a pontoon.
The little livewell is what came standard....because that's about all the frame is designed to support (in addition to the passenger load. You slap a 30 gal. Livewell on it and it might swamp the first time you stab a wave. Anyone that has ever stabbed a big wave in a toon knows how quick water pressure can rip the whole craft to pieces. I see it all the time.
My recommendation for the B-buggy restoration is to keep everything (furniture, batteries, motor, fuel tank, ect.) as light as possible so she floats like a cork. It just isn't a good foundation to be loading up with heavy duty accessories and extra power on.