The AMHS will be expensive if one is taking a big rig or truck/trailer, but IMNSHO, the experience on the AMHS is not to be missed.
SE Alaska is a "whole nother experience" and the AMHS allows lots of flexibility to stay in certain spots for longer periods of time if you want. My bucket list includes taking all the routes the ferry has to offer. I've got SE done for the most part, working on the SC areas (Whittier, Valdez, Cordova, etc) and saving the Western (Kodiak, etc) routes until last.
My suggestion would be to determine when you want start your AMHS trip, where you want to stop for how long (in my view, KTN, JNU, and Sitka are worth multiple days) and when you have to conclude your trip (i.e. in Whittier or wherever you're returning to). If you get that info and pass it on to the AMHS, they'll likely be glad to propose an itinerary around the ferry schedules.