oooohh, Mercruiser tech line... now there's a number I could put on speed dial!
Shrom, I applaud you, you have analized the crap out of this, and exhausted every possibility before asking for help. here's an even longer shot than the ideas you just blew holes in...
when I had problems with my brakes on my SUV (same style hydraulic lines) I learned something new. when hydraulic brake lines break down internally, they fray apart in a fan style. the pump creates more pressure than the relief does, so, it is possible (slightly) that the lines are breaking down internally and fanning out creating back pressure on the relief (down) stroke. couldn't figure out why my brakes were sticking, turned out the inside of the lines were holding pressure. worked fine when on the pedal, but would hold pressure and keep the pads engaged when off the pedal. only way to test that would be to unhook the lines at the pump and rams, then check flow both ways. I just don't want to see you replace pump, then lines, then rams, then check valves, and so on, trying to fix it. just guessing again...