I tried running a 2 into 1 carb with a 38mm Keihin PJ on my lightly ported 350, and I could never get it to run right. I tried mains from 150-200, as well as adding a powerjet to try and get enough fuel to the engine but it just would not make a clean WOT run. It acted like it ran out of fuel, but the bowl wasn't dry...I never had any issues with it starting, idling, revving or blipping the throttle, but it would choke and die about the time I got to 3rd gear. I honestly believe it just couldn't deliver enough fuel, fast enough, for the ported cylinders...I tried 3 different times to get it to run with the 2 into 1 setup and failed every time. lol I still have it if anyone is interested in buying it. I hear that the needle makes a big difference in how it runs, but I didn't see how the needle would have any impact on the issue I was having, so I never tried changing the type of needle.
May be what you need though, to change needles or adjust the one you have. I adjusted mine to no avail and my problem never went away...try richening the needle to see if your issue gets better.
Just passing on my experience, if you get to a point where you just can't get it right, throw two carbs on it and I bet your problem goes away, it did for me, lol