1. I'm disappointed by the cranks. They are constantly coming loose... ever so slightly, but enough for me to feel it. They develop lateral play that requires constant attention. They have to go.
2. I tried installing my THM Clavicula cranks. They looked beautiful, but there is simply not enough clearance in the bottom bracket to accommodate the oversize spindle. It rubs on the internal wiring creating significant drag... and will likely damage the wiring in time. This was disappointing as the cranks looked great on the bike. I will likely install a set of older FSA SL-K cranks I have until I can come up with a better solution. Perhaps regular DA 7900.
If all else fails, there's always the DA cranks. Albeit a little porky, but will work flawlessly.
3. Rear shifting is still problematic. The Red cassette is installed without a spacer between it and the hub. If I am on the largest rear cog (lowest gear) and apply any kind of power, particularly out of the saddle, the chain skips and pops to the point I am nearly pitched over the bars. When pedaling smoothly, seated, in this gear, it still drifts off the cog and the chain skips between the largest two cogs. I took a close look at the setup on my workstand and noticed something strange. If I shift onto the largest rear cog, the derailleur seems to drift back outward (toward the next cog) after a few pedal revolutions. This causes the chain to jump between the cogs. It almost looks like the derailleur is auto-correcting to an ideal location about 1mm outboard from the cog. I believe installing a spacer behind the cassette will resolve the problem. The only way to keep the chain on the cog is to hold the di2 button down. I don't have this problem in any other gear.
The 'Spacer' is essential.
Noticed that you've got steel dropouts ? Then suggest changing your rear skewers for a change. Get one of those high clamp force ones like Shimano / Campag / Fulcrum / Mavic ones. Its a problem I've seen with a few steel and titanium bikes. The skewers clamps do not have enough 'biting' force to clamp securely onto these harder dropouts. Essentially, once under load the wheels get out of alignment.
Follow the Di2 rear shift procedures exactly to the 't'. It often makes the difference as its a little different from traditional shifting tuning.
Basically : Tune the gears before toying with the end-stop limit screws.
4. Front end. The custom fork/steerer came loose once. I think it may have been the change in temperature affecting the bolts. Regardless, it was a simple thing to preload the headset and tighten up the front end. No big deal.
Check the 'Starnut' in the steel steerer. Many of these are of poor quality and made more for aluminium rather than steel steerers. They will not be hard enough to bite into the steel steerer tube and as you tension, they just slide along. I had this problem with my Colnago CT1 years ago as it was using a steel steerer carbon fork. I eventually got a good one from a Chris King headset that didn't use it.
5. Brakes. I am really dissatisfied with the Zero Gravity brakes. They are a pain to set up. They refuse to remain centered. And they just don't feel that good. I tried installing my M5 brakes with some improvement. The front is superb. But the cable routing to the rear was optimized for the ZG brakes. Using the M5 in the rear requires a circuitous routing of the brake cable and increases drag markedly. I may go with M5 front and ZG rear which looks horrific but should function well.
I've found ZG to be pretty finicky with the cable length. Using Nokons, it was like 1 connector too long or too short and it would not happily stay centered. But if its just right, it seemed ok.
In general, the bike is wonderful. The fit is fantastic. Everything Rob constructed is as advertised. A few of my component choices have proven to be sub-par. But I can't blame the builder for that. di2 is leaving me underwhelmed except the front shifting which is divine. There is something absolutely beautiful about the auto-trim feature on the front derailleur. Regardless of rings, the front shifts perfectly every time. Hopefully the added spacer in the rear and a change of cranks/bottom bracket will improve the drivetrain. It's a shame really, because the I want to love the Sweet Wings cranks. The bearings are smoother than any other crankset I own.
The DA cranks can be smooth too, you just need to swap out the bearings for a set with low contact seals. (Be it ceramics or otherwise.)
Hope the above will be of help. I've had Di2 on my bike for for 2 years now, had my fair share of
moments ... but all turned out well once I learned the quirks.