We did a walk-on ferry recon in October in preparation for our planned cruise next summer. We took the ferry from Anacortes to San Juan (with a stop at Lopez), had a cup of coffee at the little coffee shop next to the terminal, then onto the next ferry to Friday Harbor for lunch. A couple hours later we took the ferry from Friday Harbor back to Anacortes. Even though it was rainy/foggy it did give me a good opportunity to check things out and get a real feel for distances as I'd never been there before.
Our plan is to put in at Cap Sante in Anacortes (probably sleep there the first night as we're driving up from Oregon), sail to Spencer Spit the first day, then Friday Harbor the second night (marina/showers), and we'll sort of play it by ear from there. I'd like to go up to Sucia or around to Roche Harbor but I'm not sure we'll actually go around the outside on this first cruise or just stick to the inside. We're also not firm on the date yet - we're thinking around the 1st of August.
I can recommend OpenCPN for charting/tide/currents - it's free and uses free NOAA rnc or enc charts. I've also got "A cruising guide to Puget Sound and the San Juan Islands" and a Maptech Chartbook of the San Juans so I've got a set of compact paper charts (a capri 22 doesn't have a lot of room for big charts).