The 4.0 release changed quite a lot of files. We don't have a method to patch files or an individual change log, as that makes support and debugging of new issues almost impossible to resolve. Patching individual files also bypasses database updates that can happen in new releases. I don't think 4.0 had any, but the upcoming 4.1 release will be adding new tables and changing quite a bit about our database requirements.
We recommend if you're going to modify files in any extension that you take notes as to the changes you're making so that when upgrades are required, you can easily re-integrate them. We don't recommend bypassing our installer though for ensuring that you're fully upgraded to the newest release.
Should you run into any issues with upgrading, or need information on where some functionality you used in 3.4 may have moved to in 4.0, if at all, feel free to let us know.
Thanks,
Alex