In the following two sentences that I wrote:
After many years in which no progress was made, Tony found the first red stone. Since then, several other red stones have been found.
is it better to use "had been made" instead of "was made"? or "were found" instead "have been found"?
It's good as it stands.
Avoid the past perfect. It has its uses but it's rare, and it is even more rare to find a context where the past perfect is needed or better than the past tense.
You use the present perfect to talk about how things are now as a result of events in the past. So this is a perfect fit for "have been found"
