I would not recommend rebuilding a 95 model engine it's 20 years old and will probably need more repairs in the coming years. There is a sale on Yamaha motors at the moment pm me if your interested and I can price you up on a new engine and possibly trade yours in.
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You need to get your batteries, charging system and battery switch tested. You should have one deep cycle battery installed as well as a starting battery.
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Post some pictures of what you find and how you re make the floor. I have made a couple of them before but I have to do the floor in my Stacer soon and I'm looking at changing it from ply wood.
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HDPE you can pick it up in a 12mm sheet for about $150 a square metre. And you will never have to worry about doing the floor again. 2mm or 3mm alluminium will not have the structural integrity to be used as a floor.
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The jockey wheel uses a worm gear to turn a threaded rod to raise and lower the trailer. When the wheel is all the way up the rod can completely unthread and come out. You should be able to fix it by taking the weight off the wheel and and trying to locate the internal rod in the top section with the thread in the bottom section.
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If there is no oily residue around the rams you probably have an internal leak check that the pressure release screw in the side of the trim unit is tight. If you are worried about it or if it gets any worse the pump assembly would need a reseal.