A bit of a necroposting here, but if you'd like to see an example of how someone accomplished turning 3.5 into a classless system, go take a peek at this link . Of course, he ditched the D&D magic system and replaced it with the Arcana Evolved magic system, but it was well balanced and allowed any AE or D&D core class to blend together just fine. Replacing the magic system was required to make it so there were only 2 advancements for spellcasting.
I would probably want a bit more information about 4E before attempting something like this myself, but let us know what you come up with
