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One hull it is fine, but the other hull has warn the ridge completely down. Is this something I should be worried about?
Short answer: no - it's not anything to worry about.
Long answer: The weight of the rudder assembly is carried by the deck lip and the two lower gudgeon holes (see below)
Minor differences in the placement of the gudgeon can cause more of the weight to be supported by the deck lip. It will wear down until more of the weight is carried by the gudgeon itself. It's not a problem - and the height difference between the rudder assemblies (probably not more than 1/16") is not a problem either.
On your second question, I think you've reached the end of the threads on one (or both) of the bolts. If you still have the stock nylon nuts, you can't get them tight anyway.
Here's what the racers do: Throw the stock nylon nuts away. Go to the hardware store and buy 4 5/16"-18 stainless steel nylock nuts:
Make sure you're not running out of threads on the bolts (buy new if you have to). Re-assemble the rudder into the lower casting and tighten the nut until the rudder will not drop down under its own weight. Back off the nut slightly until the rudder just drops under its own weight. Do the same with the upper casting / tiller arm (drops under its own weight). You might have to tinker with the settings if it's still too stiff or works loose as it wears.