If you can only get your alttium project partially into KiCad, then
may have some pointers to fix issues.
Also, do you have much experience with altium?
I once looked at a project made in altium, and imported in KiCad. (worked quite well).
It was one of the Nucleo boards from the ST Microelectronics website.
I noticed that some of the fine pitch parts had their pads in an irregular spacing.
I am suspecting that Altium rounds coordinates to the nearest mill or something like that.
Is that so? Does altium always do that, or is it only in the Gerbers? or could it have been some setting in that project that was faulty?