i was thinking about putting a valve in the air tubing from the yeast bottle to the bubble counter to possibly adjust my bubble count. is this a bad idea? should co2 be allowed to flow freely between the 2 bottles?
Sounds like a bad idea. If you were to accidently close it, or it were to get back upped up, you would have an awful mess on your hands. I had air valves on mine, but only isolate bottles during mixture changes. I think trying to adjust the bps count on a DIY system is not really feasable. It is going to change constantly anyway as the mixture ages, and then you change the mixture.
Your best bet is to use 2 bottles, stagger the mixture changes, and experiment to find what mix recipe / time frame gets you the most consistent bubble count for your tank.
Never never never try to regulate the flow on DIY CO2. It's a great way to end up with an explosive mess. With DIY CO2 you control the amount of CO2 by adjusting the number/size of bottles, your CO2 mix, and/or diffusion method.