ok for how it got so dirty.
the reason it gets so dirty is because of the egr valve and the pcv valve, not you filter that has very little to do with it. the geniuses over at ford thought by putting a teflon coating on the back of the throttle plate that it would help prevent this. well i got news it didnt.
manifold cleaning
when you clean the TB and EGR passage you are correct that you do not want to let the crud get in the intake manifold. But if you are trying to clean the manifold themselves without removing them, you would use berryman b-12 in one of the vacuum ports(you prob already know this). when you are cleaning the manifold yes some stuff will come loose and go into the combustion chamber, but this is ok as long as it is not a huge piece. since it goes into the combustion chamber it gets burned up no harm there.
what i recomment you do instead of just those two things would be this
1. instead of cleaning the manifolds while they are still on remove them and clean them. all the info on this can be found here
intake rebuild
2. since you are going to be cleaning the throttle body you are gonna have to remove it. since you are removing it why not optimize it while you are at it the how to is here
throttle body optimizing
also at that mileage you should replace the PCV valve if you have not done so already for info on this pm or im me
all of these items will help greatly in improving performance, mileage, and throttle response.(PCV will only improve mileage)
if you have any questions about how to do any of these things or just in general drop me a pm or im me @ jackelcrazy. i'll give you any info you need