I don't know if Bondo brand epoxy is much good under water, but is likely OK for use above the water line. Bondo products are not designed to be immersed, they are intended for car bodies. Check the label - if it doesn't say that it's good under water don't use it there.
You can get WEST epoxy from any boat store, I like Hamilton Marine in Maine but West Marine is OK. Get the cans and the pumps to go in them, and a bunch of little plastic cups and exam gloves. The WEST system includes various fillers - so it is versatile and there is no question about it being marine-grade. On the other hand, the stuff is expensive.
It is handy to get stuff with the filler already in it. I haven't used PC-7 but I would consider using it after Jeff's recommendation.
As for the outboard mounting board, I would:
rout the edges to a nice radius
drill holes oversize and fill with epoxy/filler
saturate with liquid epoxy using a disposable brush
then sand smooth
Lay 6 oz. glass cloth on top and saturate, working around the edges as much as possible. It helps to trim, slit, or pull out fibers to get around the radius as far as possible.
when hard, turn it over and do the other side.
sand the fuzzies off.
using fiberglas tape or cut strips, cover the edges and overlap the glass as much as possible.
Redrill the holes to the size needed. This leaves the hole lined with epoxy, not endgrain.
paint to suit.
I have done this a lot. Frankly, I don't have the patience for it anymore, and I would buy a piece of StarBoard and make a plastic one. The plastic is heavy but lasts forever.
1975 32' Flybridge Sedan, twin Perkins 6-354 diesels, 1:1.53 velvetdrives, 16 X 19 props. Merritt Island, Florida