i have seen big lifted samurais with big axles out there mudding

Yeah, but they weigh A LOT less than your Trooper.

So i bet this little trooper with a big motor and 39.5 x17 boggers is going to realy kick some ass out there in the swamp.

Rocks or not, tires that big are not going to be friendly to small axles. The Isuzu 12-bolt in the back of your Trooper is stronger than a 10-bolt and the general consensus is 37's being the high end max, with 35's being a bit more of a conservative max size.

Good Luck!