Yup, Label connections, relays, for future purposes, download the wirediagram, and label the left coil connector, and the right one. that way future coil related projects doesn't matter which coil is plugged in, just which one is going to fire on the correct side, like you planned. Seems some people will mix it up, the relays one is a safety, and the other is for the headlights. Its probably good to keep them on the right circuits. I know when I am planning on going deeper into the depths of the motor, a baggy is allways cool, a piece of paper to note what it belongs too. of coarse there is the Pizza cardboard method too, the baggie works fine for me. Keep a copy of the manual close, read 2 to 3 times, so that might reduce some work, Double check anything that could be put in backwards, (I did put in my clutch rod in backwards)
Check locally acquire-able locations for parts, I have a voltage reg from the local autoparts store, and recently I found that I can get the Oil filter from there too(ch6003). For web purchases, If your going to spend $10bucks for shipping, might as well get everything you need from one site. I have been making Wishlist on this web site, seems to be less expensive here than locally/other sites.
http://www.powersportsplus.com/ Download the parts manual, so when you call locally you can guide the parts personnel straight to the page with the part on it, or you can give them the part number, and try to one up them once in a while. Check Amazon occasionally, they have surprised me when ebay didn't have something. Sometime time soon, I want to take everything I have printed out, and stick it into a 3 ring binder, and leave room for the small things to be left in the baggies, like the spare screws, o-rings, gaskets as well. A nice camera to upload pics, we all love pics!