Congrats Azygos!
There is a wealth of information on this site regarding C-Brat trips to Alaska. I would recommend curling up with the book "River Horse" which is about a trip across the lower 48 in a C-Dory written by William Least-Moon as I recall.
I would recommend that your tow vehicle have heavy duty mud flaps over at least the rear tires if not the front as well. Roads up here are a bit rough and we regularly hear loud rock "pings" that will wake up even the deepest sleeping back seat driver.
A decent front bumper with a grill guard would be a worthwhile investment as well; some of the critters you may encounter can take out a one-ton truck if you are moving fast enough. There are also a fair share of inebriated drivers after 8 pm or so near small towns as there is not a whole lot of other entertainment options so it's worth starting early and then parking for the night around six or so.
As to boating in SE Alaska, I would recommend asking around the town you are launching from before heading out regarding local danger areas and "hidey-holes" to pull into in case of bad weather. The Harbormasters around SE Alaska can have weird hours but they are knowledgeable, also try the boat supply places that the commercial fleet hang out in. So long as they know you are not a Charter Captain, the commercial guys are very helpful. It is always helpful to know where to pull in and wait out a storm, depending on where the weather is coming from. Just don't make any jokes about working on a fish farm.
Although a firearm helps against bears, bear spray is cheaper and easier to haul around. It is also very effective in close quarters. Of course shotguns are a bit more comforting when a critter is giving you the eye.
El and Bill with Halcyon Days
http://www.geocities.com/bill_fiero/index.htm have explored all over up here, they have some great stories on their site.
More than anything else, plan extra time or fewer ports of call. You can always add on at the end. Rushing around up here tends to invite trouble. We just lost two visitors who tried to push their luck flying into Sitka on low fuel despite warnings.
Enjoy Snoopy-C, she's a great boat!