Can one get the universal joint on the steering shaft to close to the headers
The way my new rack is located and the best way to connect everything will put my universal joint 1/2 inch from my headers. I concerned about damage to any seals in the joint.

I would venture to say that if you have 1/2" that would be sufficient. As long as there is an air gap between the headers and u-joint and air can flow freely around it, you should be good to go. Hey, consider yourself lucky that you have that much.....some designs or installations don't have that much. You could also check with the manufacturer of the u-joint and ask their recommendation.