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1. On the early 5.2's, how do the daggerboards get tensioned to stay up? There is no hardware around the dagger boxes to attach the bungie tensioners that I have seen on other Nacra's online.

A bit of shock cord from the top front of the daggerboard to a hook on the top of the hull in front of the front beam.
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2. The jib hardware is different than what I have seen online. I have two padded cables, one on each side of the tramp that look like they would be used to hook your feet under when hiking out. There are pullies mounted halfway back on these that look to be for the jib lines. There are no tracks or cars for the jib on the pontoons. Do these sound like they would be for the jib control lines?

Those blocks are for the jib sheet yes. The blocks are supposed to slide back and forth on the line with a control line to the back beam and a shock cord to the front beam.
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3. The padding on these lines is degraded...looks like a cat practiced sharpened its claws on them. Where can you get these pads?

Go to your nearest hardware store and get some stiff pipe insulation. It should do the trick for a while.
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Any advise on mods, sailing the 5.2, or cat sailing in general will be appreciated.

Put a spi on the thing, changes the boat...