I've got several Di2 road bikes and recumbents, but chose to build my S40 with mechanical shifters and brakes. I'm using Dura Ace brifters, a 52/34 Ultegra crankset (52/36 with a 34 swapped on), and an 11-40 cassette.
How are you going to route the Di2 wiring? Put it all in the boom? Traditionally the battery would be in the seat tube or the seatpost with the Junction B. You could put that into the boom when you build the frame, but expect you'll need to drill some holes for the cables (Shimano has a couple size grommets available).
I'd suggest 160mm discs if you ride on big hills. Only the raciest of road bikes are using 140mm discs these days, and with the terminal velocity you can get on an S40 I think the few extra grams of a bigger disc are worth the greater thermal area.
I would also consider even lower gearing than your 34/34. If you're fit, that should be good enough for 6% grades, but anything steeper than that and you'll need to grunt it out. Especially with 165mm cranks that will lower your torque. I'm in pretty good shape (and 180-185lbs and I still use my 34/40 on many rides. At 15%+ I get wheel slippage, but I just pray those are short enough to muscle through (though just a little bit of wet roads brings the slipping on sooner).
And my S40 was my first FWD/MBB, though I had lots of experience on RWD recumbents, so I wouldn't sweat not starting with a T50.