No offense, but you summed it up at the end of your last paragraph. Any traction problems encountered will be due to tire selection, not frame geometry. And if you've got mud, you'll want a nice wide fork, with plenty of tire clearance. A skinny rigid fork won't cut it. Also, any advantage a 29" wheel has on singles is probably lost on a tandem.
Re: Stoker compartment. Will your wife/partner be the stoker? Ask them how close they want to be to your, um, saddle. Unless you're having a custom frame made, they'll have to deal with whatever the stock dimensions are. But if you don't know exactly what you want, custom is not necessarily the way to go.
I'd look for a lightly used Cannondale, since you'll need to replace the headset, stem, fork, and wheels right away. From there, you'll probably look at swapping seats and bars, along with a bunch of other parts as your taste/needs dictate.