Wondering if its ever been done or if its okay to convert a 4x12 cab into a housing that would essentially keep the bottom 2 speakers, take out the top 2 speakers and make that a housing for a head.

So almost like a road case that has a built in 2x12 with space to put a head above it.
it could be done, but you have to be sure the inside dimensions will work. It would probably be better and easier if you made it from scratch
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Marshall JCM2000 DSL100
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Sounds like a cool idea. When the head is small enought it should work. For a Marshall Head for example, which has the same width as a 4x12 cab, you will have to free the amp from its housing. However, this should be possible. You'll end up with an enormous 2x12 combo..may look better on stage. I'm a bit worried about the heat...I won't close the back side of the cab, at least the top half where the amp sits. If you do it, let us see some photos!
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Interesting re-purpose of a Cab, but yes you would essentially be making a large combo amp, really no different, just bigger and heavier.