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I don't think there is much you can do about stales and rejects other than adjust intensity or change pools. And I think the latter is generally more effective.
What are you getting now and what settings are you using?
On my 7079s I use 7:28:0 (scan/expiry/queue) usually I end up with 92% wu with that
290s i use 1:1:0 again 90-92% WU
Interesting. I'll try these with my 290s to see if it makes a difference. Regarding rejects, I've read that your ping to the pool server is the most important factor (along with thread-concurrency supposedly).