Did mine at 1,100 miles (posted over in Dyno section). Several folks have told me (including the owner of the dynojet/tuning facility) that these engines take several thousand miles before they are completely broken in.
So, it is probably safe to assume the following:
(1) It's ok to dyno now, will not hurt your car; and
(2) It's likely that you will pick-up some additional h/p once you have several thousand miles on the clock. I don't think this means to expect gobs of additional h/p - perhaps somewhere in the range of 5-10, from what I have been told...
P.S. Keep in mind that dyno results appear to vary widely, probably as a function of the differences between dyno type (i.e. Mustang, Dynojet) differences between individual units of the same manufacturer, variations between even stock or similarily modded cars, etc. IMHO, the dynojet produces more accurate/reasonable results, but all dynos should be able to measure relative gains...
