I believe your exhaust manifolds for the 289 will not work as the block deck is higher than the 289 - your exhaust head pipes may hit the floor pans.
This is a good excuse to buy the 351 in a '65 swap headers, I think Hooker makes them but you might try JBA as well. With power steering, you may have to buy the drop bracket. At least this was required when headers were installed on 289s with p/s in a '65/'66 Mustang.
You might find hood clearance may be an issue so you may have to get an aircleaner with a drop base and a short filter.
You can get the plugs for blocking of the air injection ports in your head. Ford has them for sure and maybe some machine shops.
You will have to determine how to get the belts, pulleys, and brackets all configured to work on a 351. The 289 alternator brackets won't work.
I have a '65 FB with a 351 but it has a Mustang II front suspension and a custom made cowl induction hood for clearance.
Regards,
Dean T