Stuck in 3rd gear is just limp mode, could be anything from a blow fuse/bad ground to a bad TCM or transmission. You can pull all the electrical plugs off the transmission or remove the TCM entirely and that's what you'll get. Quick hint: If you put it in "2" or "L" instead of "D" you should be in 2nd, which is a lot easier on it if you need to move it around. Of course I don't recommend driving it like that.
Mine suddenly went into limp mode once and it did end up being the TCM. Got lucky and found one on eBay, but I tried the Ram TCM first. It's not the same software, as WWDiesel noted, but at least I could (carefully) drive it like that until I located a proper Liberty TCM.
I still think you should try to get codes from the TCM, and double/triple check all the basics. For what it's worth I actually got the code from mine with a Obdlink MX and Torque Pro, though I didn't trust it and bought a $700 scan tool that told me the same thing... Well I guess I kinda needed a decent scantool anyway... Not sure if it would work with a generic dongle, a 2006 Jeep, or even if my 2005 is just a fluke, but it did get the actual TCM code.
Here's the Ram TCM thread (and a bunch of other potentially useful TCM info) -
http://www.lostjeeps.com/forum/phpBB3/viewtopic.php?f=5&t=70718Sounds like a newer TCM might have some sort of "Multi Flash" and would behave like a stock liberty TCM. I haven't experimented with it, so I can't say for certain. I'll have to look for them next time I go treasure hunting at Pull-a-Part!