I would take the muffler off for starters and then see how the new carb you said you are getting works. Then got from there, drill the jet bigger one size at a time. :shrug:
Somebody once told me to think of an engine (doesn't matter big or small) as a air pump. The more air you pump in and the more air you pump out the more power you will make. So since you are sucking in a bunch of air with the ram-air setup you will need to move it out the header.
But
If it still is bogging because of getting too much air I would try decreasing the size of the end that sucks in the air. You could even put a PVC end cap on the end of it drill a larger (big but smaller than the diameter of the hose) hole in the middle of it to decrease the air intake.
I am by no means guaranteeing that this will work, this is just what I would do to try and make it work. Don't continuing doing this unless you feel you want to, because I don't want to be responsible for something being broken or spending extra money on your project.
Good luck with what ever you decide to do. :thumbsup: