I use this forum all the time for troubleshooting on my iPhone and MBP, so I figured I may as well sign up now that I have an iPad as well.
I actually bought the dark grey synthetic smart cover at the time of purchase of my iPad 3 because I didn't think the leather ones were worth the money. I found the tan leather one (my first preference) on ebay for under $50 so I bought one a few weeks later, but was a little disappointed with the way it looked once it was on the device. Google turned up this article where some guy used coffee to stain his smart cover, and I loved the way it looked. I actually achieved the end result by rubbing in motor oil of all things (another article described using olive oil but I imagine it would go rancid after a week or so) then topping it off with leather conditioner.
Congrats on getting the desired look you wanted! Does the smart cover have a noticeable odor now though?