Re: 1966 289 build
Oversized valves will definitely increase flow. If you are planning to get a valve job the installation is essentially free.
Part of the reason 289 heads are restrictive is because of the dimunitive size of the valves. Any work you do on the ports will be of limited value with stock valves.
BTW switching to a roller cam can be fairly expensive unless you have a later model block.
1966 Falcon, 347 stroker and C-4