I think maybe you answered your own question. Sounds like a ball trough issue. Check the connections to it. Could be failing optos.

There aren't any optos in the trough of a TZ.

After the "phantom drain", are you hearing the solenoid fire(the one that kicks the ball over into the trough)? If so, you'll need to check that main outhole switch. It may need adjustment, or a wire may have popped off and is touching the other one, thus triggering the "phantom drain".

As for the ramp diverter(the ball drop crane, as you called it), it is programmed to activate a few times until another switch/target is hit in the game. Start a game with the glass off and run a ball up there. As soon as the diverter fires, hit one of the 5Million targets. If it keeps going, you've got an actual problem, most likely with the opto on that ramp(at the end of the turn around). If it stops activating after you hit a target, everything is operating correctly.

Report back with your findings!

Ugh, you're right, was thinking it was the same as IJ. Should have checked my game first.

I had a short in a switch on the grey blue/black line before that was causing the game to drain randomly. You may have a similar situation. Also TZ gets confused if the magnetic sensors aren't working properly sometimes.

There is a proximity switch in there. I just fixed mine for strange behaviour as you described but my powerball wasn't registering and making it to the power field and other glitches.

After turning it on, put it in switch test mode and leave it for a hour and listen for any beeps, or bang on the playfield. If you hear a beep check what it says for the last switch pressed on the display.

? leave it for an hour ?

Yes, just let it sit in switch test mode. You should not hear any beeps while in switch mode. If you do, something like an opto is flakey.

Again, there are no optos in the trough of a TZ. There are no optos in TZ that would give a signal to the computer for a drained ball. They are all lever switches. All the optos in TZ are used for the loops, the right ramp, the mini playfield, the VUK, the gumball machine, and the clock.

While I agree with letting it just sit there in switch test mode to look for flaky switches(and nudging does help reveal them sometimes, too), I don't think there's any need to just let it sit for an hour before diving in. Because the switch that is possibly flaky is a mechanical switch, it'll be flaky from the get-go. When you start the switch test, take note of the switches that show closed on the screen and compare that to the switch matrix in the manual. That'll allow you to take an inventory of switches that are doing what they're supposed to right out of the gate.

If you do run these tests and nothing has changed, I'd pull the apron off and physically manipulate the switches by hand, instead of just using the balls, to check their activation points or to see if something is holding one of the switch arms down and not allowing it to reset back to its open state. Also, it might be a good idea to "play" a game with it with the apron off to watch at what is happening under the apron when it does the phantom drain. That way, if the outhole switch is the culprit, you'll physically see the kicker arm fire. It is fairly important while "playing" a game with the apron off to be very careful and be ready to catch the ball if it goes towards on of the outlanes.

Double check that the outhole kicker arm is not interfering with the outhole switch, too.

If that doesn't show you any new or useful information, it's time to prop the playfield up and start tracing down wires, looking for loose wires or shorts in the daisy chain.