It is nice to read Lee that you are concerned about tracking of your affiliates, especially since many sponsors still use cookies, not considering that most surfers protect themselves from such.

You wrote:

"My main concern is making sure clicks that affiliates send are tracked 100% of the time and, hypothetically, lets say the server with the affiliate program on it goes down, using linking codes with sponsorname.com in the url is a bad idea but, at the same time, if the server hosting the paysites go down, using the individual site domains in the URL is a bad idea."

I think Lee you are worry too much. If the server with your paysites goes down, I would think you would prefer no signups during the downtime, avoiding the quick refund demands.