I doubt that flushing had anything to do with it.
Do you have a digital tachometer connected? If so, what's your idle set to? As I recall (and I won't swear to this), my F115 is set to idle at about 700rpm.
Check your fuel filters as well (or just change them out.)
Make sure when you pump the primer ball that it firms up and stays firm (if it doesn't you may have a leak somewhere.) If it goes flat while you're running the motor, you may a fuel line restriction.
Barring those problems, you may have a faulty low pressure fuel pump. I do not know how you'd diagnose that, but pumping the primer ball while running will be a good indicator of that problem (assuming it goes away while you're pressurizing the system by hand.)