I have done Contour clutch replacements both ways. My preference? Definitely pull the engine/transmission out the top together! Dropping the transmission out from below by itself was a pain -- getting it back up and mounted was a struggle I wish I could forget!
I found it relatively easy to pull the engine/transmission together for the clutch work. That way there's plenty of room to work and you'll have a super-easy time installing the headers with the engine out.
Picked out a clutch yet? My recommendation is to stick as close to stock as possible. The OEM SVT Clutch/Flywheel/Pressure Plate/Slave Cylinder are a pretty robust combination. Aftermarket 'performance' clutch kits are hit-and-miss.
As Rara mentioned, there's no need to uncork the A/C system -- tie it out of the way and it'll be fine.