I'm glad Lindy chimed in. He knows the area a lot better than I do and is a wealth of knowledge.
I Also have a spare vehicle/ truck if Lindy's is in use. I've got a bunch of mechanical tools, a little bit of mechanical know how/ can cobble most things together, and a large collection of pretty organized junk like fasteners, boat parts, epoxy and other boat building junk. If I'm out at work my wife would gladly let you into the shop/ help you out.
There's a bunch of USFS and state park cabins all the way up the inside passage if you want a night off your boat. Some are more popular than others and I believe they are released 6 months out. They are a step above a tent though don't have running water or a kitchen. Most require a dinghy. The 3 semi close to Juneau with float docks are 8 fathom (about a 1/2 mile walk to the dock) near Hoonah, Kennel Creek between Tenekee Springs and Hoonah, and Tauku Harbor about 20 miles south of Juneau. 8 fathom is really nice, Taku isn't bad though the harbor can be busy, and I've never been to Kennel Creek.
There's some public float docks though not a ton. Swanson harbor has one and is roughly half way in between Hoonah and Juneau. The Swanson harbor area is our go to day trip area for halibut.
My understanding of our bag limits are X per day, X in possession, if it's packaged and frozen it doesn't count. Almost every town has a place that will package, freeze, and ship your fish to the Lower 48. Halibut and rockfish are in season all summer, salmon is really going to depend on the area. I think we are done attempting to salmon fish in Juneau before the end of June, non resident King salmon fishing was shut down last summer. Dunginess crab are everywhere, non resident limits are pretty generous. If you like crab bring a pot or 2.
Juneau is the biggest town in southeast and a good spot to plan a couple day resupply. You are going to want a car to get around. There's some stuff in walking distance of Aurora harbor though I'm not sure how much room there is for transient boats. If you do end up down town Harri plumbing is actually a really good boat parts and tackle shop. There's a costco many boats stock up at. Auke bay cafe has good breakfast across the parking lot from Stater harbor.
We've been down to Petersburg and really liked the time we spent there. It's a small fishing town and nowhere near as touristy as some places, it doesn't fit large cruise ships. The harbor is huge, really nice, and full of commercial fishermen. The Mexican restaurant is the best we've had in Alaska. Their hardware store stocks a lot of boat junk as well with more up stairs if you ask. Almost everything is walking distance from the harbors. The Wrangell narrows are a neat stretch of water and remind me more of a river. There's crazy amount of turns though aren't a problem for something great Alaskan sized. Everyone really likes the Yamaha dealer in Petersburg, Rocky's.
I wouldn't plan on the same route going north and south. There's a ton of explore and see, lots of history, some hot springs, and a lot of fish. Please feel free reach out when you think you'll be in Juneau. Hopefully my Tolman will be in the water this summer.
