Headers are the best choice but there are drawbacks to everything. My preference would be long tube headers, short tube headers, and HiPo cast iron manifolds in that order.

The iron manifolds will provide a more stock look that many like. Headers require periodic bolt tightening to prevent leaks.

The HiPo manifolds have the exits to the rear where the standard manifolds have the drivers side routing the pipe under the engine to the passenger side for a single exhaust.

I'm not a big Flow Master fan due to the interior droning at some cruising speeds. Your mileage may very. Muffler choices are very personal. I'm getting too old for the loud hot rod sound even though the Hooker Max Flow mufflers I have now are far from quiet.

Buy a tailpipe kit from Summit Racing (part number FLO-15807). This is a tailpipe set for a 65 Mustang with 2 1/2" pipes. This is the hardest part of the exhaust and will help your muffler shop. Just hang the tailpipes, attach the mufflers, and then add the section from the engine to the muffler.