WOW. That Youtube video was very interesting.
First, You need to slow down the motor speed a bunch. Way to fast if that video was in real time.
Second, You have your game set up, so that you have to hit the center target of the MPF before you can lock your balls. This is evidenced by the lock lights flash, when you finally hit the center target. I assume it does this with original board too.
Third, I am confused by why the logic circuits kick the balls out. The ball goes in, the Opto is working and sees the ball, then it triggers the coils to shoot it out. This is like there is a Multi player game and you have chosen the option to eject the balls.
Fourth, I see that you are manually playing the game with the glass off. Do you have the micro-switch in the upper left corner of the cabinet closed with a piece of thick cardboard? Otherwise, the MPF will not operate with this switch open. But I did see it go up and down on start up.
Fifth, What errors come on the screen when you boot up? CW/CWW motor errors sometimes mean that the motor either wired backwards, but you say it works fine with original board. So I coming to the conclusion that your 2nd and 3rd adjustments are off.
I had similar stopping at mid levels on my first try at adjusting the Potentiometers. I slowed the speed down first. With the two adjustments back at zero. I turned the second one up 1/4 of the way. Then did the same with the third one. I wrote down my notes somewhere. There is a sweet spot on the adjustments.
When You have it adjusted right. It is a sweet idea. Imagine being in a multi ball, the MPF is all the way up, You are shooting into the Dalek doors. You have two completed and just need that last one for Jackpot. The MPF times out just as your ball hits into the doorway. The MPF on its way down is stopped by the ball. The motor and gearbox are trying to bring the MPF down but can't. If you don't have cliffy's on the front of the MPF, the edge of Playfield may break away or the motor will burn up or the gearbox teeth will break and jam. I have gone through 2 motor gear boxs. The past few months, I have that ball jam just as described above twice. When it jams, I worry, then I see the MPF reverse direction and the ball falls away. I keep on playing. I know that is what you want also. If you lived closer, I would come over to help experiment with your Pots.
Lastly, if your MPF rollers are gunked up with old grease, or slides that your rollers go up and down on are not square, that friction will also make the new board think there is a jam and not work. Only use a light application of silicone lube on the sliding assembly. Mine was originally so greasy, it was fouling the Opto on the bottom of the cam.