I can't really help you on the specifics of jetting...but what I can tell you is that you probably want to put the airbox back on for now. If you're already having one jetting issue, don't add a second one. Also, from everything I've been told and read, the 650 is very hard to jet for pods (even amongst CBs.) I got smacked around by enough people on that one that I finally decided against doing it on mine.
I'd get it jetted in for these "custom" pipes and get her running right-ish. When you have enough for proper after-market pipes, put the pods back on and try jetting for your final setup.