Your Commander is in excellent shape with really low miles. The mods are great and in my opinion add value. That being said, you'll need to find the person who wants one with what you've done with it. I'd say start at $30k, less if you're really motivated to sell.
I had 97 VW GTI with LOTS of engine work - bored over, blueprinted, rebuilt with the good stuff, supercharged, etc; along with suspension and other mods. Between the car (bought new in 97) and the mods, I had about $50k tied up in it!! I sold it for $7k which was basically about blue book for that model at the time of sale. It was 'worth' a lot more, but even enthusiasts who knew what they were dealing with didn't want to pay for someone else's mods.
Hopefully for your sake, the Jeep community is not so cheap!!
ETA: You scared me when I first read the title and saw you started the thread.
