I bet anything it has been done, but like said by cmaje72, its probably been on a shop level where they make/have lots of money and hire someone fulltime to do nothing but hack/tune the ecm.
My guess why it hasnt been done on a wider scale is because it (appears to be) a eprom based ecm, not flash based. The eprom is sodered to the motherboard and then its all encased into the waterproof gel. Its not like the gm computers where you simply take two screws out and can uber easaly remove the chip, read, hack, tune, and reinstall it. I think thats why it has been done so much and easaly on the gm ecm's. And the ford the same way, so many out there, I'm sure the mustang builders pretty much demanded a way to tune the ford computers. So a way was found. The jeep ecm on the other hand is gonna take a little more work to get to the chip. I would have no problem doing this, I however am nowhere near smart enough to read the code and do all that magic to where it can be displayed in a tunerpro format where I can understand it.

Anyone have a lead on any other forums I could join, or people to email to get in touch with someone smart enough to do said work?