Do you actually have a dynojet kit? If so, just follow the instructions that come with it for the jet sizing. Dynojets use a different sizing scale which makes it a pain in the ass to give jetting recommendations since most of us use Mikuni jets.
You mentioned running without the airbox lid. What air filter do you have? With a stock style drop-in k&n you can't run without an airbox lid, that's what holds the filter in place. If you have this stock style filter and want to open up the airbox you can drill holes in the lid or cut a big rectangle out of the center, but part of the lid needs to remain intact to keep the filter in place.
Jetting is all about trial and error. It's going to be different for everybody, you just gotta ride it and see what works. There's too many variables to give very good jetting recommendations most of the time. Like deadlast suggested, just try a couple sizes up from stock and try them and see what works best. Most likely you will need to go a little richer on the needle jet as well, especially with an opened up airbox. In my experience the intake on these 350's seems to make a more substantial difference in airflow and power than aftermarket exhaust does, so what you do with the airbox will affect your jetting quite a bit.