I don´t know any ones in the locations you listed. I do know that Casa Grande in Cusco is great. It is cheap at 20 soles, clean, has a good location, huge courtyard which is perfect for storing and working on the bikes. The staff doesn´t mind you working on your bike either.
Also, I read that you lived in Peru so you have probably seen Machu Pichu, but if you have not you can ride your bikes up to MP taking the route from Cuzco to Pisca and than on to Hydroelectrica where you can store your bikes behind the police station. (pretty safe because it is so remote up there.)
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