Markus you are absolutely correct, thanks for sharing your knowledge with other community members. The config files will be updated once the application's been starded and all the modules ahve been initialized with the new version, and the database has been updated. It is normal for the eCommerce config files to remain at 1650 - the version when the module was intialized for the first time, but since you do not use it (do not have the licese for it) it will remain at that version since it's not being installed anymore.
David - have you started the project after upgrading it, because as we mentioned earlier, that's when the actual upgrade occurs, and please let us know if the SystemConfig.config still contains the old versions of the modules even after the upgrade and starting the application for the first time. Concerning the port difference, it's normal for them to run on different ports, as Visual Studio and Sitefinity project manager use their own integrated webservers.
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