If it's epoxy wipe it down with ammonia water. That will remove the amine blush. Then sand. Start with 80 grit and work up to 220. You might want to consider a lacquer based primer. That will give you a good barrier under the color coat.
220 on a duck boat?!?!?
If your using a Ditzler lacquer based primer 220 is about the coursest you'd go. It's a brown primer that will etch into the epoxy. It's ridiculouly durable because of that so if you cut throught the topcoat all you get is brown.
As for letting the epoxy cure for several weeks. No need. West system is fully cured in 7 days at 70 degrees. 2 days is sufficient to prep and paint in lower temps.
Now if we're talking details, make sure the weave pattern is full before you sand. You don't want to cut into the glass when you start sanding. Give it a light sand with 80 grit and see if you have any low spots. If you do use a bondo spreader to put on another thin layer of resin then sand again. Laquer based spot putty will work fine for minor imperfection and pin holes. Then prime and paint.