That's a neat one. I bet Marty has all the clutch bits you'd need to convert this. Like Paul H said, once you have the clutch pedal situation sorted, which requires some light "custom work" to the lines if you want to use a later 900/99 trans, the rest is fairly easy and you can use basically all 900 parts.
One thing you are gunna need to figure out is what to do with your front trans mount. I am not sure what it's set up like on 99-autos, but I doubt it's the same as the 5 speeds. Well, thinking about it, you will probably just need a 99 manual trans front cover to bolt onto the 900 / later 99 trans, but I am not 100% sure on that.