I have not picked an end point yet and am looking at what routes might work. It is true the mileage is quite high and ultimately I may have to pick a different starting point, however there is something I like about being able to start near where I live.
Maybe start down by Fidalgo Island. If Blaine is on the Pacific, I don't see how Fidalgo Island wouldn't be. You'd also be passing by there if you started in Blaine, so you're saving some time on the run.
Messing around with Google Maps indicates that your best bet is to head over to Delaware or New York. 43 hours and 2950ish miles depending on exactly where you stop. The typical southern route between Jacksonville and San Diego is 10 hours and ~600 miles shorter. Looks like I-5 end to end is about 21 hours and 1400 miles. Doing both, as Eric suggests, is an additional half a day's riding and a few miles.
Except that's not the whole story. If you actually ride from coast to coast, you've got to return home after. (Unless you are like
Tim from Forty Times Around.) That adds a bit to the ride that should be considered. Going back home from Delaware or New York means retracing your original route. It's not an enjoyable route IMO; too many big cities and no fun roads. Going back home from Jacksonville means you get to ride through Tennessee and Kentucky. You are a very short ride over to the Smokey Mountains and the infamous Tail of the Dragon. I would take an extra day there and enjoy the wonderful roads in that area. It's a beautiful part of the country. Rapid City is worth a day or two also. The Black Hills are fantastic! I think the ride back from Jacksonville will be much more enjoyable than New York/Delaware. You'll get to see different parts of the country for just a little bit more mileage. And you'll get a second cert. Actually, a few more certs since you can easily do a BBG on the way back, or SS1000, or even SS2000, or probably a dozen other potential rides.
In fact, I'm heading up to the Rapid City area next month. I'll be there probably all summer. My RV isn't too glamorous, but it's free lodging, all the Cajun food you can eat, a private tour around The Black Hills, and free laundry facilities. No matter where you end your 50cc, going through Rapid City is the fastest way back home.