Brian - If it were me, coming from Eliot Bay, I'd take the route via Port Townsend. In 30 years I've only gone the Swinomish Channel twice, once going north and the second time going south, and didn't like it either time. One is "supposed" to go slow and not kick up a big wake; however, that's typically not for the other guys. This is a very popular powerboat route and being a channel they pass close abeam and you get stuck with their wake with no way to maneuver out of it. Not a very nice scenario. The winds and currents going the Port Townsend route aren't necessarily all that bad depending on how one works it.
I'd get an early start on Saturday catching the ebb, slack at Pt. Wilson is a bit before 11:30 am, then get out in the main channel to catch the flood going north. The morning winds are forecasted to be out of the south then the afternoon winds past Point Wilson will be out of the Strait and be blowing up toward Anacortes along with the flood from the -2.9 tide (-3.1 on Sun).
If one leaves Elliot Bay kinda late as was indicated being a possibility, it's not all bad. Head over to the Kitsap side and hug the shore to get the back eddies, power around Point No Point, then hit the Skunk Bay back eddy. If you get past Foul Weather Bluff and it's a minus tide, then either (1) beat it over to the cut between Indian Island and the Olympic Peninsula and go under the bridge. With the flood at Pt. Wilson the current here will flow north (depending on the timing). With the bridge one has to check for clearance and there isn't a whole lot of boat traffic there. With the flood at Pt Wilson this is the back eddy route. Or (2), if one misses the minus tide and can't get under the bridge then hug the Marrowstone Island shore and catch the back eddies but check the chart for rocks - there's a couple of 'em. Speed over ground with the help of the back eddies is better than at slack. I actually prefer the back eddy route vs the bridge. There is a lot of current at the Marrowstone Light.
With the long daylight hours if one isn't too late there is time to power past Pt Wilson against the flood (3.3 kt at 2:40 PM on Sat or 3.4 kt at 3:30 on Sun) and get out into the Strait a bit to catch the flood to the San Juans. The wind in the Strait starts to kick up after around 2 PM but not too bad, probably around the 14 to 16 kt range and of course part of it veers down the main channel past Marrowstone Island. The Sunday morning SailFlow forecast shows a strong northerly in the San Juans but decreasing later in the day.
Couple other notes: Wouldn't want to fight against the current through Deception Pass with these minus tides and the area around Smith Island can get pretty lumpy from the various currents. Port Townsend anchorage: avoid the eel grass protection areas.