I performed this task over the weekend. I have the same POS 2000 Flex Fuel vehicle. I opted to take the upper intake manifold off. It was a good opportunity to check/replace several items while the intake is off...EGR valve, vac lines, and clean the intake and throttle body, and more. Plus, I replaced the ignition wires and it was alot easier to route the new wires with the upper manifold off. More work probably the way I did it, but I had it apart in 40 minutes. That was from the time I pulled in the driveway when I arrive home from work (in a different vehicle) until I was done. So not too bad. Let me know if you have any questions. I'll be happy to help you out.
Ashes to ashes, dust to dust if it wasn't for my Fords my tools would rust.