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Additionally, you'll need to make a boot image by extracting one from a stock ROM with unpackbootimg, and then packing it with your compiled kernel with mkbooting.
I also thought that you could just use fastboot and the image...
I don't think anything should broken - you are creating the same kernel as stock one. You could check if file sizes match...
Its been a while since I compiled a kernel but did you change the kernel name in config file before you compiled it? There should/used to be a way to change it via .config or a make file, going from memory here but might give you something to check on. It is a linux kernel so you can check some kernel compile wiki from Fedora or such and see how the label gets changed.
Alternatively, before compiling, use the kernel config option
"LOCALVERSION" to append a unique suffix to the regular kernel version.
LOCALVERSION can be set in the "General Setup" menu.
adb shell dmesg
adb logcat