They don't look diseased just maybe old and/or frost bitten. Yes I would deadhead the pods, they can get very heavy and twist the branches into strange shapes. This variety seems to have extra heavy pods.
As far as pruning the tree, I would shorten the lowest branches and remove any crossing ones. If you can establish a central leader that would be best for the health and structure of the tree. Think of any branch lower than 8' as essentially a 'temporary' branch that will eventually need to be removed so you can walk underneath the tree. No, the branches don't move up the trunk as the tree grows they stay right where they start. It should almost be shaped like a Christmas tree, with a single trunk and branches spaced evenly around and up the trunk. From what I can see, you have your job cut out for you. If you can find someone there that knows what they're doing to get you started it would make it waaaaay easier.(I know, not a lot of help)