Great topic.
It´s here the forum really can come to help.
Take it from the basis eyey. Already a lot of good tips from people trying to help, and then off course, the basics. Everyone knows them, but following them is another story.
One change at a time!
You have pipes, and ported barrels. What have others done to achive good results? Jetting f. exe. #260-#220 seems to be the choice for upper lidt mod, ported barrels and pipes. You write "2 sizes up" putting the bike (if 00 model) at 280-210. That alone would hypotetically mean one cylinder too rich, and the other too lean = no power.
My opinion, go slow, airboxes with clean filters, std. cdi, jet it like others have done before with these mods... or even a tad richer... and go from there.
Mine has this basic mods... the rest are subtil "finesses"... and as I wrote before RS250 start going backwards in no time.
You are not very specific about the porting either.
Hope you get it sorted soon.
Alone with these basic mods, it is a glorious bike.
Have you been provided with a portmap wich you are allowed to show?