I finally got past the first problem (Error Analyzing App Version) and now I too am getting the RATE_LIMIT_EXCEEDED error. Anyway, I guess it's progress.

Are you updating WKWebViewConfiguration.applicationNameForUserAgent? If so, try updating WKWebView.customUserAgent instead and see if that works for you. (See my comments below.)

That didn't fix it for me. My command line tools are current. "softwareupdate --install -a" outputs: "No updates are available.".

version: "xcode-select version 2395". And no, I'm not modifying the IPA whatsoever. All I do is "xcodebuild -exportArchive ..." and once that is completed I do "xcrun altool --upload-package ...". The altool doesn't actually exit with an error, it just prints a bunch of python errors and then continues.

That was exactly the mistake I was making too. Thanks for posting your suggestion.