Adding CTI ports is similar to adding IP Phones. You can just add them in Call Manager and associate them to the JTAPI user. This should not cause a server restart. You will also need to add them to a CTI port group within CRS.
You didn't mention the version of UCCX, however, I believe all versions starting with 4.x require that you build the CTI ports within UCCX. The UCCX server will then build them in Call Manager. I would definitely do it after hours.
I can tell you that I had a problem with "out-of-sync" ports because they had been built by out integrator on Call Manager independent of UCCX (we use 4.0(5)).
Are you getting this error “Installer User Interface Mode Not Supported. The installer cannot run in this UI mode. To specify the interface mode, use the -i command-line option, followed by the UI mode identifier. The value UI mode identifiers...
The below trick might come handy when you have to add a new node to a cluster but you don't have or is unsure of the security password for the publisher. This procedure has been around for ages.
1) Login into the CLI of the Publisher.