When you add larger valves, and you have a professional machine shop port your heads, they are in no wise stock... LOL In your case, I say if you port your heads, they are not "stock". You can say the "stock heads have been home ported by me".
Stock is a standard valve job, maybe new guides and new springs. The end.
You might as well say.... I sent my STOCK cam in to get reground for better performance, but I'm still running the stock cam. Ummm, yes, you are, but not anywhere near the stock specs.
