In looking through the forum, it sounds like the new Spinergy tx2 wheels may be a good option. Thoughts? They would definitely shave quite a few grams off your stock 40h wheelset, perhaps 1.25 lbs p 1.5 lbs per wheel, and also give the bike a more comfortable, lively feel.

Should I upgrade the brakes? Some fresh pads would probably help up front, but much of what you're experiencing is just adjusting to a tandem's added weight. The "Travel Agent" V-brake adapter is also part of the front brake feel issue. The best upgrade would be moving to newer Ultegra shifters where the brake pull has been adjusted to be correct for V-brakes & discs without any type of cable pull modification. But, now we're getting into some serious $$.

Any ideas on whether this is a good carbon fork? It's a Santana-branded / house fork and Santana tends to err on the conservative side so it should be both robust and reliable. Also bear in mind, you've got a 1.25" headset, not a 1.125" so your fork options are limited unless you install a Devolution-type headset that reduces the 1.25" to a 1.125" steerer fit.

... and it doesn't appear that any of the suspension seatposts can be low enough to accommodate her riding position. I'd definitely ditch the suspension post. As for trimming weight elsewhere, it's a cost / benefit thing. You can easily get this bike down to the low 30's, but you'll put $1,500 into it quickly to do so.