I was an early poster in this thread and figured I'd share my general update:
I don't seem to get the "spinning search wheel of death" that lasts for 10 minutes anymore. I didn't do anything that would have fixed it, so don't know what to say there. Instead, searching often fails by coming up with a list of blank emails with date stamps of 12/31/69. Some searches work correctly now, some don't - I have given up trying to figure it out. It honestly seems very random.
I had also reported that it wouldn't search my non-icloud (imported) emails, but starting a few months ago it seems to have gained this ability. Again, I don't know why. This is only a minor victory however, since searching is still so buggy overall.
Search on my iphone has always worked correctly.
I also have the false "unread messages" button on my VIP list as Peter describes. And then it randomly goes away...
For good measure, other icloud issues I have in Firefox: I have the opposite problem of TimFinni - when I try to scroll the body of the email, it moves at a snail's pace. Additionally, I have some emails (i.e. emails from Groupon) that DON'T HAVE A SCROLL BAR AT ALL! Literally, you can't scroll down the email using your scroll wheel, but it does work if you use the arrow keys on the keyboard. These absurd issues seem to be specific to Firefox, so I'm not sure who to blame.
In summary - this thread appears to have no consistent theme that would point to "the issue". It just seems like an overall shoddy/beta service by Apple. I'm just taking it day by day and hoping things improve. I did submit reports to Apple awhile back.