So, I decided to take the boat out and take it to the local marina shop who has top notch service and a couple of big tanks that they can put the boat in to test it out. I'd go through the troubleshooting myself, but my travel schedule just doesn't afford me the time to go through that. I think it may be the scupper and here's why - if my wife and I stood on the swim deck, then every time the bilge pump cycled it would pump for 20-40 seconds and then stop. On the next cycle, it would do the same. It did that 6-8 times, so it seemed like it was slowly refilling when weight was towards the back and possibly pushing the scupper under water. If my wife was on the deck alone, then it would cycle but not pump. I didn't see anything more than 1/2'' of water at the very bottom/center of the bilge at that time. As soon as I went back to the deck, it pumped water again.
When I took it out, I didn't have much time to troubleshoot - other boats at the ramp, but when I did pull the plug, it drained at a pretty good rate. During my 1st two years with this boat (and keeping it in the slip), I can't remember ever having a drop come out when I open the plug, so that's new.
Anyways, the shop is going to call me in a couple of days and give me an update. They are the local dealer/marina at the lake and have wonderful service - they are Cobalt, Malibu,...dealers. The Yamaha dealer, while they do quality work, is woefully understaffed and can't do timely work (took them 3.5 weeks to install Perfect Pass, add a 2nd bilge pump with float, and do a start up).
I'll post an update later in the week - thanks to all!