Please take a look through the STTNG thread https://pinside.com/pinball/forum/topic/sttng-owners-club there is tons of advice and mods listed there, and please let me be the first to welcome you to the club!

The tieback wire was not the best engineered design but its far from a bomb waiting to go off. What I did on mine was 1) did a professional soldering of the wires to start with (this should be enough) and 2) used heat shrink tubing over the wiring and coil terminal. Truth be told, I did this to nearly all of the coils since I rebuild the wiring harnesses and already had the tubing and a heat gun.

Disassemble, clean, rebuild and inspect ... everything. Game is now flawless

If you do take that much of the machine apart to replace all the emitters, you may as well go ahead and replace all the photometers as well, as these are really inexpensive to replace.

I think I need to tie a red LED to the extra ball insert lighting and have it shine up through the mission hole...anyone done this or have opinions on it? Maybe even a second white one to the start mission light ...

I don't doubt this as they do have a very low failure rate. My thought on it is this:

1) it will cost less than $10+shipping to buy 25 photometers.
2) they are extremely easy to replace, should take less than 1 minute to remove and replace each one.
3) it will take you the better part of the day to take enough of the machine apart to replace the left orbit emitter why not spent the extra minute to replace the photometer while you are there.
4) If you are going to replace one because you have things taken apart to do so, why not just do this for all of them?

This is just my thought process on the matter ... others may feel differently.

You should do this for sure!

http://www.marcospecialties.com/pinball-parts/CS1713

You will probably also find when doing this that the parts were greased at the factory ... subway and Borg diverter ... now have hardened grease and this old grease is impeding the diverts ability to operate smoothly. These should be disassembled, cleaned, and have a TINY amount of new synthetic grease applied. https://www.amazon.com/Super-Lube-21030-Synthetic-Grease/dp/B000XBH9HI/ref=sr_1_1

Please ignore anyone that says grease should never be used in a pinball machine ... these are metal-on-metal parts and are an exception to the general rule.

Yes and no, the software I think you are referring to runs on the COLOR DMDs controller board; this is a small board that is part of the color DMD and has nothing to do with the machines software. You have to download the game specific software from the ColorDMD website and install it with a USD drive, it's pretty straight forward.