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Shifters (this'll be one of the thumbshifting ones)
For shifting you can also use XT Di2
Junction box (any particular one, or are they all the same)
https://www.bikeparts.co.uk/products/shimano-sm-ew90-a-e-tube-di2-junction-a-3-port?
If you want to be able to see the gear you are in you can use the Alfine or XT/XTR Di2 one.
SD50 cables
1 short cable from shifter to junctionbox at stem/handlebar
1 long cable from junction box A (stem) to junction box B (https://www.sigmasports.com/item/Shimano/SM-JC41-Di2-Internal-Cable-Junction/WI9)
1 cable from junction box B to battery (length depends on where the batt will go)
1 cable from junction box B to alfine motor unitBattery (what's the difference between this and the external battery?)
This is the external battery: https://www.probikekit.co.uk/cycling-electronic-components/shimano-di2-sm-btr1-battery/10781871.html?
It comes in 2 or 3 mount options depending where you want to mount on the frame; https://www.wiggle.co.uk/shimano-bm-dn100-battery-mount?
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amey
PhilDAS
So of that I've already got
Batt charger
Motor unit
you need:
Shifters (this'll be one of the thumbshifting ones)
Junction box (any particular one, or are they all the same)
SD50 cables
Battery (what's the difference between this and the external battery?)
External batt