Yeah, I actually used cmk_fi_ks as a starting point (not in the beginning, but at one point when restarting my xkb config project). My goal was to get all this to a single file which would not require me to change any files provided by the xkeyboard-config package. I'd like the files managed by the distro's package manager to be left untouched, unless they are config files under /etc. Now I have a single file that I can drop or link to /usr/share/X11/xkb and everything just works.
I actually hadn't read your Extend topic, just peeked at the keyboard layout pictures. I read it now, and I still don't think modifier keys, like your Extend layer does it, would be super useful for me on the home row. I use the i3 window manager for which e.g. Alt-F4 means nothing. Text selection in Emacs is quite different from today's desktop text editors, and Shift is not used for that.
For me, the most important feature is to get easy access to Control and Alt (Mod1) keys in combination with letter keys, because those constitute almost every key binding Emacs has.
With Control on the Caps Lock Key, I have Control-X/C/V in comfortable positions, and having arrows with the Caps Lock key pressed is enough on the occasion I use something else than Emacs for editing documents (e.g. I'm writing this post in Chromium). Now that you made me thing about it, having Shift on the home row could make that experience better, but I'm not sure where to put it to not sacrifice an important Control + letter key combination.
With i3, I've mapped many window managing keys behind Super (Mod4), and that's why I have Super in the QWERTY B position. It could be changed to somewhere more comfortable, but on the other hand, I can always reconfigure i3 to adjust the Super bindings.
About the key repeat bug, have you reported it somewhere? I thought about writing to the xorg mailing list about it, I guess someone there could have some insight into what breaks it.