James, all good questions! I am actually trying to get some assistance from the resident sound experts on how I should proceed. You can see a more detailed description of the setup here, http://www.thechainlink.org/group/bikesound/forum/topics/boom-bike-... .
This topic is really just to find someone to build the steel trailer since I have no welding skills.
Regarding the trailer question and the batteries be sure and communicate the weight issue to the builder. I have a lot of experience pulling trailers in the automotove/truck world although not much with bikes.
Batteries are fraking heavy so that is going to be an issue both with the trailer's frame and hitch arm as well as the hitch on the bike too.
Don't forget about the weight bias on the trailer itself. You want to have sufficient tongue weight (but not too much) or the trailer is going to want to push the bike around something fierce. On an automotive trailer you ideally want something close to 10-15% of the Gross Trailer Weight on the tongue of the trailer. This becomes even more important as the weight of the trailer gets to 50% or greater than the weight of the tow vehicle which most surely be the case here unless you are a super big dude with so much audio gear and the power supply.
Getting the balance of the trailer so that you have 10-15% on the tongue might be tricky with the batteries where they are. Talking with the trailer builder about these things and knowing what each component weighs and where its individual CG falls on the trailer footprint will be important to get tongue weight correct at the design phase. Re-engineering the weight bias after the trailer is built and it rides horribly will add unnecessary expense and time to he project which are things I'm guessing you don't want.
Good luck. It's a neat project and I'll be following that other thread to see how it progresses.