So your original harness had the adapter "flylead", and 3 wire plug for the GPS?
But the new harness has a 4 wire GPS plug?
Hypothesis:
Wondering if your bike being a 2013 build might've had the early Roadster wiring setup.
Which had a 3 wire GPS.
And the 3 wire GPSs were faulty.
So previous owner upgraded it to the new 4 wire GPS (standard on 2014+ Roadsters), which would require the fly lead to adapt the 2013 harness to the 2014+ GPS.
But it also would have required a reconfiguration of the tacho wiring.
And now you replaced the harness with a fresh one, (2014+), which they supply with a 4 wire GPS but also a flylead which confuses people, leaving out the adapter flylead is causing an issue.
If the answer to both questions is yes then I'd say we need to reconfigure the tacho wiring so it matches the 2014 harness/4 wire GPS.
Sorry for jumping in and interrupting your process TURBO200R4 , just seems like given bike age a photo of 3 wire GPS this might well be the issue.