It could be worse it could be a watch. Good luck.
So far it definitely isn't running like a Swiss watch :(
Patience, perseverence and a little care is all that's needed (a 16BA nut spinner is usefull as well if you can find a good one. I haven't yet). Take it one small step at a time. A loop of set track (mine's Egger but I believe that Peco are now making OO9 set track) helps as you can watch it run around in circles after every stage, which is usefull for troubleshooting.
I don't think I've ever checked and re-checked parts so often before but it definitely pays dividends to check carefully. For testing, fortunately Jerusalem is a nice oval of N guage track with enough clearance for the motor unit at least, and I've found the rolling road I bought when I first got back into modelling last year is great for getting a really clear view of things moving (or not).
That does look a little brain-damaging !