If the frame is rotted your first step will have to be stopping the rust either buy chemical or abrasive means till your down to good clean metal.
At this point it gets fun. What your going to need to do is build a frame around the damaged section using good steel and cut or grind 45 degrees on the edges of this 4 piece box frame that your going to build around your older frame. making sure the new frame parts have an 1/16 to 3/16 gap (.0625-.1875) this will allow the weld to bond to the orginal frame section as you weld into it. A "fish plate" welded to the frame and to the new section will add ridgidity. ( a plate about 8 inches long and 1/4 smaller than the frame width, extended between the new frame section and the old.)
I would recomend good mig welding for this and a welder who knows what he is doing since you need GOOD penitration here.
After its all welded up a good undercariage primer and paint to coat the inside and out.
This is the best fix at this point.
I would recomend you look over the whole under carriage at this point and think about doing a red dye inspection for cracks along the whole frame. you might want to concider that your frame is rotten all the way through and look into a replacment. Your pics showed that you love to play submairine racing with your Jeep and after 14 years of this there might be more damage than what is visable at this moment.
Quadratec sells replacment frames at a very good price.
