You can't create KR-MDS scenario by simply mixing those two mods, KR and MDS are not compatible. You can't just copy and paste MDS fles over KR scenario or vice versa. Events, minister IDs and other important elements of those two mods are not compatible.
How to create KR-MDS game? If you're going to make AAR with such game, it's worth to make such scenario to gain attention of readers. As for personal enjoyment, it's not worth of your time and energy.
First of all, you won't get self-standing scenario where the game is ''playing itself''. Original MDS event chains would be mostly ruined. It will all depend on your conception of storyline. You must make the storyline by yourself.
Basically, core of MDS-KR is MDS mod (I prefer to use newest 1.6 Beta MDS scenario, check in forum thread to get it, it's compatible with Armaggedon, it isn't for Doomsday as old versions). Elements used from KR are mostly only gfx stuff and such (mostly flags and shields). All other stuff is from MDS.
To make your unique MDS-KR (well, only this option is avalible, as ''generic'' official version doesen't exist), you must mod your MDS game. Go into scenario files, change alliances, relations, map, nations, leaders, politics...really a lot of work. It depends on that how do you imagine KR world would change in 60/70 years. Then you mostly mod MDS scenario, use a copy of your MDS game of course, as original MDS scenario would completely change.
Elementary, MDS-KR is only heavily modified MDS scenario. KR elements that are used are mostly gfx (flags/shields) and storyline concept (authoritarian European monarchies, Syndicalists and others are still around, of course you can make a scenario where Syndicalists were already defeated or something else). I hope this helps a bit. No real mod is avalible yet, all of us KR-MDS AAR writers didn't create real mods, we are making changes in scenario files, save game files and in game. This is very chaotic and unstable way of modding, but for making real KR-MDS mod, well organized team with a lot of time, energy and modding abilities would be needed.