The chain was even degreased, washed down with water, then relubricated and our current problem arose well after this was done.
Degreased with what?
Washed down with what? (high pressure)
This process isn't that complicated. I definately appreciate people that what to do the job right and maybe even better than Honda recommends. You can never be too accurate.
However the flaw with what you're doing is that the rear sproket has 2 things holding it. One bearing through the axle and a bunch of rubber pieces. Even though everything is held pretty tight, I doubt that it will be more accurate than the marks on the side of the swingarm.
Here's my guess on the noise, you used solvent or something on your chain to clean it. Then pressure washed it and re-lubed it. Using a pressure washer will remove lubricant behind the o-rings. Spraying chain lube on it will not penetrate that far back into the chain. Chain lube does help your chain but it is nothing compared to the lube under the o-rings. ( I used a non o-ring chain on my track bike and lubed it after EVERY session, It lasted 6 track days)
I hate to say that I think your chain is porbably junk. Your chain has to be either extremely loose to make rattling noise (which is more likely to jump teeth ) or your sprokets have to be out of allignment pretty far. (the swingarm marks are close enough to keep that from happening)
I would suggest wd-40 to clean it, it will disolve the old chain lube and also doesn't hurt anything. Then wipe it off. I know it won't clean your chain perfectly but it depends on how much you want to wipe. Then it will fling off a little too after you ride but I haven't thought of anything better that won't hurt anything.