I would agree that a per download basis would be far wiser, and would help eliminate some of the problems. There are of course factors that would need to be taken into account ahead of time to prevent abuse starting up again.
First one I could see, would be that you would need IP tracking being used, as well as a system in place to prevent automatic downloads.
Second,would be that only one download per IP address should be counted. Yes, people might not get the file the first time due to errors, but you've still been paid, you shouldn't get paid for their reattempts.
Third, would be to continue hand inspecting the logs before payout. This should prevent people from using an internet cafe etc to generate huge download counts since a large amount of IP's from the same area would throw up a large warning flag.
I would also definately agree that the rating system needs to be tied to the comments. I know for myself, that I've got a bunch of five star ratings that to be honest, I would love to know why they rated them that high. My partner and I work hard on each of them, but I Know they're not perfect. Having the comments linked to ratings would be a good way to know if it's people just rating things high because they feel they should, similar in principle to giving only positive feedback in galleries, or if they really like things that much.