1. What type of connector do I need to connect my trigger wire to the 5 amp aux leads? I have one orange trigger wire but it looks like two leads on the aux wire? Is there only one way the connector can fit? Which side is hot?
I believe on the Standard/Tourer the hot is the green with red tracer. On the Interstate, I think it is another color. The ground is the solid green wire; so it's the other one. To be sure just check it with a test light with the key on.
As far as attaching the wire to the accessory wire on the bike. If you don't want to wait to order a bullet connector, you can just strip the wire upstream from the connector and wrap, solder, and shrink wrap the connection.
If I remember correctly, on mine, I simply put a small flat head screw driver in the split part of the connector and just spread it open a bit, that way, the slightly bigger bullet connector will fit. I put a drop of solder on the connection as well, just to be safe.
2. How do I get to the leads without damaging the plastic cover?
It takes a little finagling, but the plastic cover will slide up. As already stated, it is easy if you open up the wire bundle tie.
3. What are my best mounting options for both the fuse panel and relay? Attach them with screws or other means?
I used an Eastern Beaver box on mine, which I believe is taller than the Centech box. I just velcro'ed it to the top of the battery box lid (works only if you have a Standard or Tourer). Makes access to the box very easy and it stays out of the weather as your ass is covering it most of the time. The relay was wire-tied to the area in front of the battery box.
4. What do people mean when they say they mounted the fuse panel behind the right side cover? How is it mounted?
That's better left to the people who have done it that way. I know some mounted it on a plastic base and tied it to the frame rail. But again, I didn't do it that way, so I may be telling it wrong.
5. Should I wire up the relay and fuse panel off or on the bike?
I did it on the bike as it allows for proper wire lengths, placement, etc. But YMMV.
Good luck.