..... I have snorkels on 4 300's all with 1 1/2" pipe , all were no problems , never really needed to adjust the carbs , now my 450 needed some tweaking of the carb with the snorkel , but it has a air box that is not the stock air box and it has 2 inch pipe ------ did you try to run the engine with the air box cover off and then with the air filter off
------ Friday I helped my friend put a snorkel on his Yamaha 400 and it was easy to put it on but the bike didn't run worth a crap afterwards , it was spitting and sputtering , the bike ran fantastic before the snorkel , I had cleaned and put a kit in the carb a few weeks ago for him , we tried adjusting the carb and it changed the way it ran but never got 100% right , he rode it yesterday with us and as we rode we played around with a rag and duct tape , tried 6, 5, 4 and then once we put three layers of a terry cloth towel taped over the snorkel inlet and taped it , then it ran great , from what I have seen Yamahas are very temperamental on the air supply , but Honda 300's for me are not , he is going to try some different sized bushings in the end of the pipe to act as an orifice , and is also going to try some metal screen and the fiber filter used on wall unit a/c 's to see if he can lose the towel
another thing I can thing of is : where is your crankcase vent running to ? if it is running into the air box and you have a lot of blow-by then maybe it is affecting the air mix
How about a pic of your set up