What spoke pattern did you use? OP's bike has 2-cross. When you feed a spoke through from the outside, the spokes on the other side prevent it from being turned up to the rim. How did your around that?
If the first cross is the one just a centimetre or so from the hub flange, then mine too is a two cross pattern. I just guide the spoke as soon as it is through the rim into the most suitable gap in the opposite side's spokes, and work it gently into place. I have in this way managed spokes that pass through the flange in both 'in to out' and 'out to in' directions.
It takes care to protect the rim from the spoke end to prevent scratches, and there is a fair amount of temporary unstraightness, but I had no trouble. There was far more trouble getting the centerlock disc and cassette off without the proper tools!
Obviously my 700c on a normal hub rather than a hub motor has longer spokes and will be a bit easier, but my 26 inch old MTB wheels probably have same spoke length as a 700c hub motor wheel, and they look feasible to me.
But maybe the pattern is not as I think it is.