For me, starting a new game with JeremyCor's download (and a host of other mods) produces a scary error, which after digging through the log appears to come from a bunch of MissingMethodExceptions on the method ProtoPartResourceSnapshot.get_maxAmount. If I continue playing, KCT appears to mostly work fine - it gets nonzero build times for ships, the launch button is disabled from the VAB, the build function adds to the build queue, and clicking on the launchpad opens the KCT UI instead (where I can edit the settings, since the scary message replaced the default settings prompt). However, clicking on the runway doesn't appear to be overridden by KCT - I'm not sure if it should, since I never played with planes.
EDIT: it appears both the launchpad and runway work, but only after at least one saved ship exists in the relevant directory. I guess the order has changed so now the "no saved ships" override happens before KCT's.