On a 4x4?
Here's how I do it
1)Look at each 2x2 on each side and see which has the most 2-colors.
2)Pair them up intuitively.
3)I know my color scheme inside out
4)I try to swap around 2x1 blocks.
5)Or try K4.
5x5.
I see your problem. Again you CAN try K4. Try to keep track on some of the pieces while forming them. Try to visualize how pieces will form when you turn layer/slices.
Okay, I've spent some time working on your problem and doing some calculations. These are the four solutions that I have developed, to fix your problem. I suggest following all of them.
In the wiki (and posts about FMC) they are always talking about pre-scramble moves. But there is no explanation of what they are. Of course they can't really be illegal, or else they wouldn't be widely used.