See the link below - I think there should be some seal. Its been a few years since I had mine apart - my knuckle bearings were shot too. The seal there is to keep oil in the knuckle. The pumpkin has seals to keep the oil in the gears. These were designed to run with oil in the knuckle, which lubricated the wheel bearings, knuckle bearings and u-joints.
That said, if you pack all the bearings with grease, (I have been doing this since 2009) you don't need oil in the knuckle, and then could probably get by without a seal. If it were up to me, I would try to have the seal there - it's really your inner wheel seal - it will keep out dirt and water. More so if you go off-road a lot.
As to the clunk, it is hared to say. I would jack it up, see if there is play in the wheels, or knuckles, spin the wheels and turn the knuckles to see if there is any binding. Twist the tie rods using vice grips to see if any binding or noises there. It's not a noise from the wheel stop on a full turn? Tap around with a small hammer to see if you can replicate the noise. Sometimes, the spring bushings can make clunky noises too.
You've got a nice truck there - good luck with it.
http://www.junkyardgenius.com/JEEP/A...dknuckle01.gif