Congratulations, you have chosen a fantastic pin.
When you have time, be sure to check out the STTNG owners forum, you will find a ton of useful information there.
https://pinside.com/pinball/forum/topic/sttng-owners-club

You may be able to fix this by squeezing the mounting tabs on the actuator arm with a pair of pliers

This is a 1N4004 blocking diode, it is required on all switches to prevent the active column signal from propagating to other columns.

hard to say, with this switch out of the loop, the game will think the drop target is always up, if its supposed to be down for staging or ball locks then the game will be firing the drop coil. You may also be hearing subway firing to sent the ball to the proper location, this is less likely as unless the machine is staging, balls in the top hole should be fed to the upper left VUV which requires no subway diverters to activate

I believe there are two shuttle craft animations, one shows a shuttle craft leaving UFP HQ in San Francisco, this is activated by closure of subway opto SW46. The other is just a shuttle craft and is activated by closure of the switch at the top of the right ramp SW87.

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A lot of these are cracked in that spot as its the main shot to advance in the game; plus if you raise your playfield without removing all the balls, the staged balls will slam right into the plastic ends of the subway. There are metal subway protectors available to help with future breakage; for a player quality machine, you can post in the STTNG owners thread to see if someone that has an old subway leftover from a restoration project that they would part with; but if you are planning on a full restoration (new quality or better) you will want to replace it for sure.

New Quality or better:

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Are you referring to the linkage that contains the setscrews or the diverter itself. These parts were well designed and should come right out, if it was incorrectly installed and the setscrews where tightened down outside their slots, you could be dealing with metal burs on the shaft. The pictures I provided should help in this area as you can see all the parts removed and how it should look when put back together.

PRO TIP:

Best cleaning method for the Stainless Steel Subway insert (ball track) is to go over it with a 3M Scotch-Brite Fine-Finishing Sander after removing all the crud.

https://www.amazon.com/gp/product/B00004Z4DK/ref=ppx_yo_dt_b_asin_title_o06_s00

I used this on all of the upper playfield ball guide rails as well as the subway track.

I almost forgot...

Please look over this post for more detailed information on bulletproofing the subway diverters.
https://pinside.com/pinball/forum/topic/sttng-owners-club/page/53#post-4768297

This is what I use on metal-metal moving parts:
https://www.amazon.com/gp/product/B000XBH9HI/ref=ppx_od_dt_b_asin_title_s00

Ok. I'm still confused on this as you aren't taking the shaft out of the crank (part that contains the setscrews), you are pulling the crank off the shaft. You should already have the plunger of the coil, if not this is why its difficult.
1) First remove the 2 screws holding the coil stop in place, remove the coil stop, then slide the coil out of its plunger
2) You should be able to get the plunger out of the coil retaining bracket, if not remove the retaining bracket and spring.
3) Now slide the crank off the shaft, if it doesnt want to come off, just hold the diverter so it cant turn and rotate the crank back and forth while applying upward pressure until it comes off.
4) now just pull the diverter and shaft out of the bushing, if it's stubborn, feel free to smack it with your rubber hammer.

Essentially, it should look like this before you remove the crank and diverter shaft, as you can see in the picture below, I cant recall if I hat to remove the coil retention bracket to get everything free, or if I removed it since everything was coming apart anyway.

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The stock coil should have more than enough power to make the shot. If after the rebuild you are still having issues you may be seeing some ball bounce from the ball guide to flipper transition, there should be none. After your rebuild, put a straight edge against the ball guide and align the flipper bat to it. If the straight edge cannot rest against the entire flipper bat AND the ball guide with zero gaps ... Make it so!

My best advice to you is to become familiar with your switch matrix test (T1)

This is what the switch matrix should look like after castration (balls removed)

STTNG Switch Matrix-no balls (resized).jpg

You have to bypass the high power interlock by pressing it in; this game didn't come with "pull-out to bypass" interlock switches.

Lowest price on these can be found on ebay:
ebay.com link: itm

wiggle the connector pin the photo transistor board, if the switch closes then it's a problem with the header or connector, if nothing happens then it's likely just a bad IR LED which is repairable.

Exactly correct.

If it were me, I would measure the voltage drop across all of the IR LEDs. A reading of around 1.5V is good, 12V is bad, 0V is worse.
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A lot of folks out there will suggest removing this board and looking at the LEDs with a camera so you can see the IR LEDs glow, and I have to admit there is a certain amount of coolness in this, especially if you've never done it before; however, it takes less than a minute to make all 7 measurements and in reality you can just place the black lead on any ground point and just move the red lead to take all 7 measurements.

In reality the best adjustment for this game is to ignore the hole completely and just put a straight edge along the inlane ball rail and then adjust the flipper (with rubber installed) so that its flush to the straight edge.

Bally Williams games were designed to have the back edge of the flipper (without rubber) aligned to the pin that goes in the hole.

Stern games have the hole out further and you align the center of the flipper to that hole.

I've worked on a set of optos like that before ... what I found was someone replaced three of the IR LEDs and broke the thru holes on all three; this was causing intermittent connections and was difficult to find.

Exactly the same, you may have to bend the ball guide rail to get it to align perfectly. When its properly aligned there will be zero ball hop on those time you let the ball ride by; and will be against the flipper when you go for the Delta Ramp; this is the single most important alignment for consistantly making the Delta Ramp shot.

Can go this route if you so choose ... https://www.pinballlife.com/full-flipper-assembly-for-williamsbally-machines-from-021992-to-101998.html Jusat make sure to order the correct one