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Kaypro 2x with a Gotek

Are you saying you updated your Gotek with the "debug" version that logs to the USB stick? I have considered doing this myself.
If you can boot off the floppy with the gotek as B, and your boot floppy has PUTSYS.COM, then you should be able to "sysgen" a gotek image in "drive B", and then flip back to the gotek as drive A and boot.
I can and have installed the Gotek as B and booted off A. This is how I know some of the images on it are good as I have run some of the programs. I do not know if my boot floppy has PUTSYS.COM or not. Will have to check. Thanks. So I would need to have a blank images in the Gotek to do this? Or will it create everything? Oh, you mean to have the image I have tried to boot but was not able to boot and it should make it bootable. Got it. I think that is what you mean.
Yes, the "sysgen" process (on most CP/M's, including Kaypro) is independent of files stored on the disk. You could take a WordStar distro disk and "sysgen" it to make it bootable (although that was not recommended in the old days, as one wanted to keep the distro diskettes "pristine").