The price of an ATX to MTX swap is almost as much as the difference you'd pay trading your car in for a new one...except if you got a new one, you'd get a reset warranty (no warranty on the MTX swap), new hidden 04 features (like a larger sump), and you wouldn't have all the hassles of a half assed conversion.
For example did you know that even the radiator between the ATX and MTX differ? The amount of stuff being replaced is just phenomenal, not to mention the amount of things that can be "broken" during the swap.
I know, I researched, found out it was cost prohibitive, and traded my 6s ATX (03) in for a 6s MTX (04). Using S-plan, and available rebates, you can get a 6s MTX for around 18-19k (bare bones). Trade in value of a 6s ATX is around 16500 to 17000k if your under 30k miles.