This could be a mechanical or electrical problem.

1) Does the Ball Count unit operate smoothly up and down when you activate the solenoids maually?
2) Does the Ball Count unit Reset solenoid activate reliably when you reset the game?

The Trough switch is responsible for resetting the Gate relay.

I would say it is the player up unit in the head of the machine. If it is gummed up or moving sluggish it was cause all kinds of issues balls not counting same with points not counting on the right player ect. Very common issue with Bally Games.
I always clean the shaft an borad with 90% alcohol an a scotch brite . Then put a thin layer of spray silicone or some Super Lube.. either will work.
An as said before
Trough switch or the outhole switch might be out of adjustment for the gate..

If everything was ok until you did the work I think it's unlikely that it's the PU. Get down and look closely for switches that might have gotten caught by the towel. The M/B on Game Over might be one to look at.