to make helping easier, you guys can find the twin joker schematic in:
http://bingo.cdyn.com/machines/bally/twin_joker/resources

the schematic symbols are a bit different. The shuffle (shutter) switches appear to be drawn when the shutter is closed.

assuming the ball lifter stops when all the balls are out of the trough, you've either got the manual ball lift push button switch stuck closed, or the ball lift relay is not working right. With the balls out of the machine so you can lift up the playfield with the power on:

- push down the "shooter alley" rollover - that's the ball runway/lane switch in bingo terminology. The ball lift relay should power and stay powered
- lift the ball gate flap (rebound gate) at the top of the runway. The ball lift relay should unpower.

it's the ball lift relay that turns the lift motor off/on, and there's the index ball lift motor switch that keeps the motor running until the lifter arms has reached the bottom again.

if the index ball lift motor switch was stuck closed, the motor would always run unless the 1st player tilt relay was tripped. That doesn't sound like your problem.

the twin joker schem is not linked into the web pages ... kinda like all the stuff at
http://bingo.cdyn.com/machines/bally_one_balls/
which ya don't know about unless someone tells you. I have a few more one-ball manuals/schems to stuff there one of these years.

ignoring for the moment that the ball lift relay should power/unpower just using the alley switch and gate switch regardless of what the motor is doing....

if:
- the #1 ball trough switch (pin switch) is good, which you said it is
- the motor stopped when a player tilt relay is tripped,
- motor runs always otherwise,
your index ball lift motor switch is probably stuck closed. In bingo land, that's the ball lift carry-over switch.

above the ball lift motor is a bracket with a couple switches. The one furthest from the motor left/away from the cabinet side is usually the carry-over switch and it's job is to keep the motor powered until the lift cycle completes. The switch rides on a cam, and there's a notch in the cam that lowers the switch stack and opens the switch when the lift arm is all the way down.

I fixed the picture on this page:
https://bingo.cdyn.com/techno/howtheywork/insidebingo/ball_lift.html

if that switch is ok, make sure all your plugs are in the right places.

you've got the switch state right...sounds like you're stuck at the "normally" part. On the schem, the switches are usually drawn in the "not doing something" state - typically at game over or right after reset.

the index ball lift motor is shown as normally open, and that's when the motor is off.

shortly after the motor turns on, tho, the #1 ball trough switch will open because the ball sitting on it got lifted. Without the index ball lift motor switch closing, the motor would stop with the ball only lifted a short way up the chute.

the lift arm has to go all the way up and down to allow another ball to roll into the lifter and close the #1 ball trough switch again....the curved metal arm hanging below the lift stops a ball from rolling into the lifter chute during the cycle...which would be unfortunate for the lift motor gears.