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If all of the plugs are installed, where did the 4-5" of water in the splashwell come from?

With twin 60's on the back of a V-20, it should be lighter, not heavier. If the boat has been sitting around for awhile, it could be rain water that is finding it's way back to the splashwell or it could be that water ingressed while backing down aggressively or even a bad drain tube.

I would drain and re-launch the boat in the water to see if the problem persists. If it does, start with the obvious areas being drain tubes plugs being properly tightened, bilge hose siphoning in water, etc....