Friday Harbor is a shorter distance to Stuart but if you "walk-on" with your boat to Orcas, you could paddle from there to Blind Island, camp, and from there to Jones Island. From there it's a long day to Stuart but if you are feeling lucky, you could shorten the trip by staying a night at Posey Island (very small, it may be full; hence, luck - but kayakers are usually accommodating).
If you get to Stuart, be sure to get your shirt. Along the way to the lighthouse at the west end (a day hike from your kayak campsite) there's a school and right near the path is a "booth" with various tee-shirts, sweatshirts, and hoodies - with a Stuart Island logo - for sale. You can't buy them in any store; you have to pay your dues and paddle to the island to own one. All varieties are strung out on a line so you can try on sizes. Once you find what you want (color/style/size) you can get a new one in a plastic bag from the supply trunks. It's an honor system. They know you may not be carrying money so there are instructions with the garment telling you where to mail the check.
Stuart is a greater commitment than Shaw, Lopez, etc. You will want be hit that crossing channel between Roche Harbor and Speiden Island at (or just before) Slack Current - or else it can get interesting.
There are three main camp areas on Stuart, Reid Harbor, left and right sides, and Prevost Harbor (yachies) on the north side (Google Earth is your friend). To me, the left side (facing the beach) was too dark and wet. Also, many guide groups use that. The right side is kinda dry - just dirt patches. There were trees for a hammock but they were too near the pit toilet. There was one site on the right side just at the beach but you can get a breeze with a mile fetch coming into Ried Harbor (Not a bad thing if you plan for it.) So, like the three bears story, I like the third choice - the campsite on a bluff above Prevost Harbor. It has trees, flat areas, a water spigot, and a "beach" landing separate from the powerboat area. You'd paddle past the dock to just around the corner of the harbor. Especially if you land there, be sure to bring your boat up and tie it off.
In the photo below, I could have moved the kayak behind the log. But there was a kayak group that was leaving in the morning and though it's on clear in the photo, if placed behind the log the kayak would extend into the kayak loading area. I moved it behind the log (and still tied it off) after they left. Oh yes, the tide came up even higher than in the photo.
Mariner XL - no hatches. 17 feet of pure storage.
If you haven't used the WDOT ferry reservation system, that's covered in other posts. In fact, there are several "San Juan" trip reports in this sub-forum.
One thing - and I'll note that in Alex's last post - though the current is your friend if it is flowing your way, equally important is the wind direction. It doesn't take much of a current or a wind, blowing towards each other, to add a pucker element to the paddle.
You can tell Stuart is sort of a trip on its own. Given that you have other goals, maybe only consider it if your week is 7 days instead of 5. There is a lot to get to know east, west, and south of Orcas.
James Island, east of lopez is nice too and you can paddle there from the beach at Washington County Park (I think $10/day parking). Guide groups land on the west beach but there are nice campsites on the east side too.
Almost forgot, Washington County Park has showers (you don't have to be staying there to use them) - just say'n if you are going to be out for 7 days
Last safety tip - there's a water taxi service out of Anacortes, Island Express. You might want to have their number in your cell phone if you carry one.
