Quoted from Markharris2000:One word of caution: it is very likely that swapping the two wires at the two switches (#37 & #38) pictured will yield the correct playing results, BUT by simply doing so, you may actually end up using the wrong wire colors for each switch, which would make subsequent servicing needs more difficult. The best way to fix this issue is to make sure that the light-green with grey tracer is in fact connect to CN11 pin 2, and that it runs all the way to the switch for the Control Room target (#37). Do the same for CN11-Pin 3, making sure that the light green (no tracer) runs from that Pin 3 to the Pit Top switch (#38). In this way, the manual will match your playfield, making the machine easier to troubleshoot for subsequent owners.
this ^
Also my OCD would not let me do it any other way.
I think you are on track with the previous advice given and I would like to add the following that might give you a better understanding of how to trouble shoot switches, which will come in handy while you are looking at this.
I wish Stern included this manual with the machine but they don't. It is weird that they don't especially in today's market when it is mostly home buyers that buy these things.
They did a really good job at explaining the Spike platform (I am a bit of a nerd and enjoy reading this stuff).
https://sternpinball.com/wp-content/uploads/2020/11/SPIKE-System-Manual.pdf
Page 37 and around there is a good start.
Also I would recommend you buy yourself cable, soldering gun, solder and a digital multi meter. You might not use it now but you will at some point.
This job might seem daunting at first (it was for me when I started) but once you take the first step that is it.
I was looking at Spike II switches for the first time yesterday actually (had not had an issue before) fixing my own switch issue, and although I can't confirm, because I did not have to replace cables, I believe the cable from the connector to the switch is directly connected meaning it is not daisy chained like the ground cable.
If that is the case, you can easily run a new cable if you had to but this might be too complicated just yet.
If the cables are inverted at the connector, a 0.100 molex tool, like this one but not this one (sorry could not find the right link but wanted to show you anyways, this one is for .156 connectors and you should buy it for the other connectors in that size should you ever need it).
With this tool you can easily take the terminals out and place them in the right place if needed.
https://www.digikey.ca/en/products/detail/molex/0011030016/228686
Good luck