I'm in the middle of rebuilding my own. I checked pricing on Bill Jenkins site and the trans housing is almost $500 dollars as you say. My trans was riding on the frame also and I replaced the atx mount. It now rides about an inch above the frame. The outside of the case is worn from where it was riding on the frame but it is not cracked - guess i'm one of the lucky ones here! If you get a rebuilt trans they are going to charge you a core charge of 300 to 500 dollars, and when they see your case you will probably not get your core charge back.
If you were going to do the work yourself, I'd say get a new case and rebuild your trans...you still come out way ahead. If you are not doing the work yourself a new case with labor and rebuild is probably up or over 2000 dollars. You can get a brand new atx from Ford for 1800 dollars from what I seen. So it may be best to see what type of deal you could work out with a respectable Ford dealer that could give you a break on labor, etc.
Amazing what a collapsed not broke motor mount could cause...you gotta love Ford engineers...Ford tough as they say!!!! You got to wonder what was going through their head when they were designing this car with the cad software package....who actually says well give it an inch clearance here, or actually give it a .233 inch clearance over there. I love my Saturn L200. Open the hood, and there is so much room I could almost stand in the enginecomparment with the engine still in there.