You know the old saying "if it ain't broke don't fix it"
I would recommend making sure you keep a good stock of trifurcon pins, molex connectors and pin headers in your pinball spare parts stash. The common sizes to keep are:
0.156 to address things like burned GI connectors on the Power Driver Board
0.1 is good for these little connectors for your switch matrix on the MPU
Best and easiest place to order from is Great Plains Electronics:
0.1 Connector Pins (Part # 08-52-0123)
https://greatplainselectronics.com/products.asp?cat=73
0.156 Trifurcon Pins (Part # 08-52-0113)
https://greatplainselectronics.com/products.asp?cat=80
0.1 Molex Connectors
https://greatplainselectronics.com/products.asp?cat=68
0.156 Molex Connectors
https://greatplainselectronics.com/products.asp?cat=86
0.1 Pin Headers
https://greatplainselectronics.com/products.asp?cat=71
0.156 Pin Headers
https://greatplainselectronics.com/products.asp?cat=79
Various sized Molex connectors are using throughout your game so instead of stocking dedicated sizes like 2, 3, 4, 7 etc... I would get the biggest connector possible such as 15 pins. From that you can sacrifice one pin hole to cut down to the size you require. You can use a hacksaw or a Dremel with a cutting disc which should cut through it like butter and then sand the side down smooth. The same goes for pin headers too as they can often be broken down to the size you need. Keep note that Molex connectors and pins come with or without locking so be careful when you are ordering. When ordering Trifurcon pins you will should order more then you need because sometimes you might screw up and besides they are cheap.
If your old connector such as your GI is burned then chances are you will need to replace the pin headers on the board too. You can probably get away with doing the connector only but don't be surprised if it burns up again soon.
The next thing you will want to invest in is a crimping tool like this which can be found at Sayal or your local electronics surplus store.
I recently put together a group buy between some friends for this $23 Ratchet Crimping Tool from amazon.com.
I had the first crimper from many years ago from working on my MAME projects but this one from Amazon is really nice because it is does both insulation and conductor in one single crimp. Another bonus is that it is ratcheting so you don't have to worry about squeezing too hard or not enough causing resulting in a bad or poor connection.
Usually ratcheting tools go for >$50 and I believe the official Molex one is $250. I mean unless you are a professional or have an obsession collecting Gottlieb Sys80's this cheap China tool should suit your needs.