The tubes are supposed to be open to the air, hence "breather." Just cut a notch in the linked tube or cut it in half so they dangle. Some people don't event run tubes. I don't know why "Nick Haber" is fucking with you but he is.
There are 3 types of chokes found on PHBG models- pull choke, cable choke, and lever choke. AFAIK these all have to be operated manually and are not linked to the throttle cable. Better pics of your specific carb and choke setup would help diagnose.