My wife and I used to tour on separate bikes. Even with her bike naked and all the gear on mine, I still had to ride a lot slower than I wanted in the hills. That was why we got a tandem in the first place. One thing we did differently than almost everyone else was to put her in the captain's saddle. She gets a good view, as do I, and we can ride as fast as our legs will take us. Since I can see around her, some of the usual captain's chores are handled by the stoker (shifting, drag brake), which makes it easier for the small person to ride captain (5'6" 130# vs 6'2" 190#).

Too bad you're on the other side of the country. Otherwise, I might be able to talk my wife into letting you borrow our original tandem to see how you fare on such an arrangement (it will work for anyone between 5'4" and 6'3"). It does require a very quiet (stable) rider as stoker, but almost anyone can manage that with a bit of training on rollers. We also opted for 26" wheels on our tandems to deal with toe overlap issues. There are some other frame design issues to overcome, but any tandem builder should be able to handle them.

With that as background, here's my suggestion. If your current tandem can handle it, try having your wife ride as captain (after you perfect your technique on rollers). If it can't and you can afford to risk a couple grand, have a frame built that will allow her to captain and use as many parts from your current tandem as you can to minimize the investment. If it works out, you can then buy new bits. If it doesn't work out, then you may recoup some of the cost by reselling it.