[jka]

I'm not sure that any of these ideas will be news to you, but a few suggestions:

- Add test coverage for your customizations, so that after you pull upstream changes, you can confirm that your software still works (or at least runs)

- Relocate and/or rewrite the custom code within your repository so that you are less likely to encounter merge conflicts when retrieving upstream changes

- If possible, fetch upstream changes on a regular basis so that you detect upcoming conflicts early

- If possible, petition the upstream project to add support for plugin modules, so that you could develop your own customizations in isolation (albeit still with some API-level dependencies on upstream)

Are your customizations definitely specific to your own company? (a gold standard could be to publish your own software as FOSS and attempt to build a supportive community)