Doug, welcome to the board!!...I'm a big proponent of Starboard, too and it'll sure work well in the areas you're talkin' about...but I took a different route w/ 3/4" treated plywood, then upholstered w/ white vinyl...made mine "L"-shaped to turn into the cuddy about 12"...did this in '99 and it's held up well and caused no problems...
I did remake all hatch-lids outta Starboard, including the anchor hatch...the stuff is GREAT to work with and "0" maintenance...
I noticed your fuel tank vents are below the rub-rail...if you've ever had water intrusion probs, that's most likely the culprit...several of us have relocated those fittings above the rub-rail... ;)
Good to have ya on the board...glad to see ya don't mind postin' pics...we like pics around here ;)...
Oh yeah, if the ''soft spot'' is in the bottom of the well...a little flex there is probably nothing to worry about as I don't believe there's any support under the bottoms of those wells to begin with... ;)...