There are restrictions on the number of rounds total, approximately 330 without paying a duty. I do not know what the duty is. There specific limits on reloading components such as primers, caps, gun powder including black powder, and loaded rounds.
the only problems with items transported like whiskey & beer in larger quantities probably have to do with duty and or possible illegal sales. Open containers in the vehicle are pretty much the same as in the states, illegal.
To transport prohibited firearms you must go through an FFL dealer on both ends. Arctic Ammo in the Palmer/Wasilla is reasonable and Boondocks Sporting Goods in Eagle River Ak will usually do the paperwork. They all must charge for the time and risk involved logging in your firearms and you will more than likely need at least a drivers lic. From Alaska to pick up your shipped guns. I wanted to,ship some of my handguns down south but legally I can't pick them up as a non resident! You can transport hand guns and long guns on the airplane, seperate the ammo, and declare it to firearms inspectors prior to your flight.
If it is summertime on the ferry system you can sleep out on the rear upper deck in chairs or pitch a tent, but if you get off in Haines Or another road connected port, make sure you won't have to cross the border again.
You can carry "bear spray", but not "self defense" spray. Might be the same stuff, but they will confiscate it. Remember that your firearms are NOT for bear protection or self defense. That is frowned upon in Canada. I have found it tougher sometimes to get through the US side of the border rather than the Canadian Border officers.
The agencies are different like RCMP, CFC, And border officers.
With your animals you only need a rabies cert now, but I am not sure about horses. Probably a health cert within the 30 days of entry.
Be patient, polite, have your IDs and proper papers and things will go smooth and uneventful.