The Shimano Di2 Dealer's Manual pdf is easy to follow. The adjustments are easy, and the directions are step-by-step simple.

Download it here. You want the DM-UL0001 manual.

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NOTE--I don't have a tandem. Do you have two chainrings? or is there a way to use a triple with Di2?

I get clicking when cross chained 34 front and 11 rear. The chain is hitting the pickup pins on the big chainring. I never get derailleur cage rubbing.

You'll get used to the new buttons after a couple of rides. I switch between Di2 and Campagnolo thumb shifters on my other bike, and the transition is pretty easy for me.

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E-tube software

I used the free E-tube software to:

1. Change a "long press" (1/2 second or longer) to be "shift 3" instead of "shift all cogs". Now, at the base of a hill, two long presses of the bottom buttons shifts to the 34 front, and 3 harder gears on the back, just right for the upcoming hill. And two long presses of the top buttons do the opposite.

2. Update the firmware. "I updated my bike's firmware" isn't a sentence I ever expected to say!

The Di2 charging unit just plugs into your PC, and the E-tube software works through that cable. Easy.