Well woods did kinda give you the answer already. You see the problem is that not every engine runs the same. So it is hard to give an absolute answer. Try the stage 3 and adjust from there. You will probably need an assortment of jets and a lot of time. You may even discover that different carbs will need different jets. That is the problem with tuning for pods.
See the issue with your carbs is they were DESIGNED for the airbox. So it is not that just honda says it is best, it is almost everyone who uses these carbs and most any other constant vacuum carb. The proper operation depends greatly on that vacuum.
If anything, you at least got good pods and not the cheap ones. So that will help a little but once done, you may find that you do not have any extra power over the airbox.
The ride IS the adventure. The destination is just to get gas!