On the little girl build, they replaced the hard metal ducting with round flexible ducts, you could do something similar.
Another option would be to recess the batteries into the floor similar to how my water control valves were originally installed.
If you keep the stock ducting, have you considered building a frame out of angle iron, then putting the batteries up on that skid so you could slide them forward toward the wheel well?
I'm hoping to get 2 group 65 AGM dep cycle batteries into mine when the time comes. And I am also worried about weight distribution.
I am curious to know what sort of solar kit you decided to go with.
Have you started a thread on it?