I don't see why not. Just wipe the cache, dalvik cache and system. Don't wipe data.
I was able to get the stock ROM fully deodexed and booting.
I used the dsixda kitchen (0.223_rev8) and a had to use baksmali 1.41 and 1.42. I see that disxda just released 0.223_rev9 so you'll probably want to use that as it has more S4 fixes.
When you deodex you'll want to use baksmali 1.41 for everything except for framework.jar and services.jar. You can probably get away with using 1.42 for everything though.
baksmali 1.42
baksmali 1.41
smali 1.42
smali 1.41