I am building a custom tandem primarily because I've had excellent experiences with my custom single bikes (two road, one track). You just can't compare the difference in fit (for me). No more extremes of saddle adjustment or stem length. I get a comfortable mid rail seatpost postion on my saddle and a nice neutral handling stem. My wife gets a position that mirrors her single bike.
As for 26" wheels, I've owned both on tandems and I prefer the 26". We did the One Day Seattle to Portland in just over 10 hours (19.9 avg.) on our 26" wheeled tandem. That is plenty fast enough for us.
We've owned two stock tandems. We liked things about both but neither fit both of us really well. This time we know more of what we like and don't like. This time we're going custom.