I think the "3.9" suggested was meant to be a differential gear ratio, not the engine type, even though there is minimal difference between the 3.9L and 4.0L.
I made a comment about hooking the clutch up to the ECU. This does not require the changing of your ECU from an auto to a manual. The auto ECU will run the manual gearbox, but not vice versa.
If you have a peek under your dash, you will find a gray plug (female connector). This connects the clutch sensor directly to your ecu, giving it the ability to change between acceleration and deceleration modes. However, the car will stil run even without this hooked up.
I picked up a perfect condition box S/H, with a brand new clutch etc and I have had not an ounce of trouble, guess its just the luck of the draw hey.
You might want to check out reco prices if ur concerned.
In my opinion, if you are after a good performing EA-ED 6cyl, without forced induction, you will be shooting yourself in the foot by keeping it auto.
I did a few mods to my car when it was auto and still had a hard time beating V6 commos. Since the manual, beating a V6 commo is an easy task..
Just my 2c on the topic.