Bill,
If shes runnimng rough now, its going to affect the run in and cause more damage than good, so you have really to do two things regardless of where you want to go.

1) It needs to be diagnosed/rectified/setup safe.
2) It needs to be run in following your engine builders brief.

Its then up to you where you go and what you do from there on in, but an engine should never ever run badly no matter how young or old it is.

Hope this helps.