Your electric choke isn't original I don't think, but anyway, there are a couple of things that could be causing your issue. The original carburetor on my 78 has a fast idle cam right underneath the choke that holds the throttle slightly open as your Jeep heats up. The choke applies pressure to this in order to take it off when it gets warm, so this could be your issue. If I were you, I would check this linkage when your Jeep is warm and make sure that it isn't still engaged.
Also, a vacuum leak will cause your engine to have a high idle, so make sure that you didn't accidentally bump any hoses off or anything with the installation of the harness.
As a side note, I vaguely remember when I rebuilt my carb (MC 2100) that the choke housing was under vacuum. It could be that your electric choke isn't sealed perfectly against the carburetor and you have your vacuum leak there.
1978 CJ5 - 304 V8 - Twin Sticked and sitting on 35's
2010 JK- Rock Krawler 2.5" on 35" KM2's