Wow, that's a ton of stuff. I thought my alternator was bad, had it tested, only to find out that the gauges were the problem. Didn't the guy that was "storing the boat for some people" say the thing was running great? Same boat?
A little more info would help, and now I'm really curious why all that stuff had to be replaced. Basically, I'm wondering on whose recommendation you swapped all that stuff. Not that I'm a rocket scientist or anything, but it sounds wierd to do all that and not pull the thermostat, etc. The MAF thing indicates runability issues - I know the MAFs will fail in time, but now?...and with the computer and stuff but no mention of the prime suspects (spark plugs & fuel pumps)?
Very sorry to hear that you've had to do more stuff to yours than ten average S22s put together, and I really ain't trying to be an ass, either.
The good news is that I've had 3K in mine - it would plane with two adults inside, but with three, we had to lean forward a little :-) If you want to run with that kind of weight, I'd suggest going for even less pitch than the usual ACME recommendation (13x11.5). Prop that thing to where you're pulling 4,000 rpm at heavy weights and 24 mph - probably be an outstanding part of the power band. Weight fore and aft equally (-ish). I do 700 in trunk and 700 in walkway and always keep some weight under the bow cushions for trim (up to a couple hundred pounds).
Oh yeah, and get Perfect Pass (break out another thousand).