In general, the more hacks you have, the more of a headache it is to do upgrades.
I recommend keeping accurate records on any hacks or other customizations you apply, including which files are added or modified, and what changes are made to the database.
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Please also see our parent organization VNC Web Services if you're in the need of a new UBB.threads Install or Upgrade, Site/Server Migrations, or Security and Coding Services.