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Your process sounds fine. The UpgradeMODX extra installs a fresh version of all MODX files and clears the cache, so it shouldn't matter what you did before that.
Incognito (or private) mode is essential when you have what looks like a cache issue. It takes the browser cache (including the browser's JS cache) and cookies out of the picture.
[ed. note: BobRay last edited this post 7 years, 4 months ago.]