Hey Nick (mustangramair), would you quote what the instructions said...I'm just curious to see what it said exactly for the "break-in". Now I could see the valvetrain (which "connects" to the cam) would be a break-in issue. It is good to go thru a warm cycle or two to see if you got leaks or problems. Just as you have noticed with the leaks.
I have my timing at 16* at 39psi with 30lb injectors. I think with your 24lb injectors the 40psi (vaccum off) is a good place to keep it. Bump your timing up 2* at a time and see how it reacts. You will need to run a higher octane to take advantage of the advanced timing so you do not ping.
Go from 12,14,16,18* and see where it acts better...
About nosMatt's comment on being lean it was kind of inside joke I believe because I think he had some car trouble with one of his car's by going lean. If your at 40psi (vaccum off) and your fuel pressure is up to par you won't be going lean...probably just about right.
What are your plugs gapped at? I would try Autolite 3924's gapped at .045 or the equivalent.
Good Luck man