Are you talking about the 4 smaller nuts that are kind of in the middle of the skid that are for the transmission mount? Regardless, I guess it really does not matter which bolts your talking about. Sounds like they are rusted so I would try some PB Plaster on them. Soak them a couple of time and let it sit over night. There is nothing special about any of the the 6 bolts or 4 nuts that hold the transfer case skid in.
My 03 Rubicon build thread ---> http://www.jeepforum.com/forum/f22/1320quicks-03-rubicon-build-1504699/