Good on you for doing what will be a great adventure.

Read the charts and read them again. Then, have good electronics on and pay attention to them while underway. The San Juans are not open water and there are potentially plenty of places you need to be aware of as far as depth and currents, particularly in the boat you'll have.

As far as fishing, lower your expectations since you won't be familiar with the scene. Most people you will see will be trolling with something like 9 foot rods and 20-30 pound test off downriggers. As others have mentioned, there will be lots of silvers (coho) and humpies (pink) around that can be found higher up (although certainly not just the "first few feet of the water column"). Your realistic goal should be coho salmon and you are most likely to accomplish that trolling a cutplug herring behind a banana weight OR casting a medium spinning rod from the boat with a buzz bomb. Watch how people fish them. It is a sweeping or jigging motion for most and the buzz bomb must freefall on the drop. To me, this is not the place for your 4 or 5 weight flyrod. Yes, you could make it work with the mono suggestion above but, that said, you could take a tree branch with kite string and make that "work" too. Get yourself a 4 piece spinnning rod that can cast 12 pound test a long way. Buy some smaller buzz bombs, a few 4 and 6 ounce banana weights, a few dozen herring, learn how to cure and cutplug them, and then just enjoy the scenery. Crabbing should be easy. You can buy a crab ring that you can drop/pull off the boat for less than $20. Try wherever you stop but look for all the bays with the red/white buoys since those are all recreational crab pots. You can only keep males and they must be large enough.

The best thing you could do is buy a bottle of booze and be friendly to those around you when you are docked. Maybe someone will invite you out for the day and show you the ropes.

Good luck and have fun!