Yes, the topping lift has a section of bungee cord on it, it is adjustable if needed. The sister clips allow the pole to be detached if not in use. While racing, the clips stay attached to the topping lift line. They also help me untangle things if that should occur.
The pole downhaul line remains attached to the pole, even when the pole is not in use and stowed. When in use the line is run through its' fairlead and at the ready. As for storing the pole, on the DS I the plan is to store it on the side shelf. The DS II however doesn't have that available. On the DS II the pole is stored in the cuddy cabin where it can be pulled out easily for use. With deploying the spinnaker, I had to remove my hatch covers to make access to the spinnaker and pole easier. Of course eliminating my hatch cover also caused me to lose my compass mounted to the hatch cover. The solution was to install a center "stalk" to mount the compass to. It can't be easily bumped as it is recessed slightly. Having it recessed into the cuddy cabin a little allows me to put the hatch covers back on when I put the boat on the trailer.
The pad eye I used is similar to PE-3SC on the page you sent, although I got it from RaceLite.
http://www.racelitehardware.com/rl272smspri.html (the small size).
The places where I attach hardware I put a loop in the end of the line using a "saddle stitch" with waxed nylon harness thread. Something left over from my saddle building days. I have loops I put in lines 10 years ago that are still holding strong. I don't like the bulk of a knot. Hardware that I may change out from time to time, I attach by running the end of the line through the loop, cinch it up to secure it. Some hardware I attach the loop to directly. Sometimes, as in the case of the swivel double shackles (with screw type clevis pin) used on the spinnaker, I put the clevis pin through the loop and attach the hardware to the spinnaker head when the spinnaker is going to be used. I thought about using sister clips, but wanted to reduce weight aloft.
Yes, the sheets are attached with sister clips as well. I also have a ring between the sister clip and the grommet on the spinnaker, held in place with a small shackle. This gives me an option to attach the pole to the ring or just to the line, I've done both, but prefer the ring at this point.
John