The mk4 does contain the knox bootloader so the only known way to go back to mc2 is by using billards back to stock mc2 with counter reset.
Now about the possible aroma issue. I have used a few aroma scripts and even did my own custom aroma for a rom and while they had issues none did what you are talking about. The issues i have experienced were lockups when switching from aroma menu to installer and back to aroma menu. I have found one version that gave me 0 issues. If you will try this out
http://xdaforums.com/showthread.php?p=47719471. Download version 4 (4.2 contains some stock mc2 rom making it large!!!) and do something simple like changing your recovery. See if this script causes the same issues as your other ones. Hopefully not and you will now have an aroma version you can build off.
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