I should also mention that this my first power boat I had all center consoles before buying this boat so sorry if I sound dumb.

34* total timing @ 3000rpm's . We all started from somewhere and were inexperienced , no worries about sounding that way .

58 m.p.h. sounds about right for twin 260 h.p. 350 cu.in. in a 26-29 foot performance boat. My ChrisCraft Stinger 260 did 58 m.p.h. stock.
With high rise intakes, rejetted carbs (Q-jets), taller flame arrestors, Crane Cams, roller rockers, World Product heads, and larger props (23" clevers with 1:50 ratio drives)
I increased the top end 5 m.p.h. to 63 with a light load of fuel. I'm not sure where you got the info that your boat "should" run 65+. I think it would take
350 MPI motors and a stepped hull to run those speeds stock. You will need to increase somewhere in the 150-200 h.p. range to reach your goal IMO.

Just wondering will mufflers affect the performance any?

my 27 Nova 3 did 63 max at 5300 rpm. motors were built to 350 hp though. 23 mirage props. anything u do for upgrades now will probably be usable on later 383's, so won't be money wasted. vortecs aren't the only head to consider for marine use. castings are a lil thin and crack a lot. I would consider Darts or Edelbrocks. mufflers don't cost much power. my nova was TOO loud with nothing but 18 inches of hose and tips hanging out above the platform. (not the way wellcraft set it up.) when the manifolds get old, that is the first upgrade u wanna do. PLUS that's the main thing that makes them look like high performance engines.