During an upgrade, especially for clients who've indicated they wish to keep customizations, I take whatever version I'm upgrading from and compare it to the stock files of that version; then I mirror those changes to the stock version I'm upgrading to (after the upgrade has gone through).
Though the more mods the more it effects the bottom line; most mods don't take longer than 20 minutes to merge over so I include those in the upgrade price, anything more would mean an additional fee.
