These brass Hex plugs are about twice as long as they need to be ... I got them from McMaster-Carr .... I have seen some that when tight are flush or close to Flush .... Suggestions ?

try a different brand or get a tapered pipe tap and run the tap thru the manifold a little further.

I used polished S.S. plugs available at most plumbing wholesale outlets. I also bought the pipe thread taps to redo the holes in the intake manifold. You have to be careful with the aluminum, and if you run the taps to deep its harder to get them to seal but the result was the plugs are now flush.
Dave

unless it bothers ya leave it...................or.... i use aoroquipp fittings they fit pretty flush...

How many threads are actually ingaged?

About 1/2 the plug ... the 1/2" plugs are 5/8 lomg .. there's about 5/16 out ...just bugs me ....

Buy a 1/2" pipe tread tap and make them exactly as you want. Every other method is a guess and a waste of time. You can use a 12 pt socket and ratchet and skip the cost of a t-handle.