You'll have no problems with height. Semis drive it and you'll see other 43' MHs. You don't have any choices with the roads. It's either the Alaskan Hwy or the Cassier. Many folks go up on the Alaskan and return on the Cassier to try to time the bear activity at Hyder.
I will say that we didn't have the stiff mud flap across the rear of the MH - only ones behind each wheel. We had absolutely no damage to the MH or towed Jeep during our whole summer trip. However, we actually saw folks in Whitehorse, Yukon removing their stiff flaps because of it throwing rocks at their toad vehicle. We saw the layer of large stones at the base of their windshields. We came through that same section previous to them so either it was because of the stiff flap or some other reason but it was strange that they had the same damage.
We drove those construction sections slow and pulled over as far as we could to the right when an oncoming vehicle approached and didn't get any windshield dings. I really think that's the secret - drive slow and don't follow too closely to the one in front of you. You'll also see more critters that way!