as for the jetting, dynojet needles are stamped DJ, and factory pro main jets are stamped too.
Yep.. check the main's to see if that have Factory Pro stamped on them around the side. If you DO see the stamp on the mains then go and pull one of the needle jets out, if it is adjutable with an e-clip or is it is silver (titanium) its jetted with a stage 3 kit.
Stage 1 kits allow you to run the air box, Stage 3 and stage 5 jet kits only run with individual K&N filters w/no air box.
Also check to see if the air fuel mixture screw's are exposed. If you dont see a small screw (like it has an aluminum cap or coverover it) that will tell you 1 of 2 things..
1) They arent jetted (you always adjust the air fuel mixture screw's when jetting)
2) OR if you do find aftermarket jets inside ,the doorknob that jetted it didnt do it right.
They are located on the out side of the carb's but directly next to the float bowl's.
Factory Pro's jet kits come like so..
Primary jet's (sometimes)
1 or a couple SET's of Main jet's
1 set of Primary jet's
4 needle jet's
and Springs (not always)
Size of the jet's vary depending on make, model, and what stage the jet kit is.
Assuming that flow commander adjust's the air fuel mixture screw's it COULD be jetted, but that thing sound tempermental. skrooz is right though, if its done right you wont need that damn thing on there