mclark, I don't know why your carb is acting up, but probably not your pipe IMO. I am running OEM carbs on 2 Super 9 LC's with Tecnigas NextR pipes and they run very well. I used to run this carb on my People 50 2T before and after I installed 72cc BBK. It worked great, but went to Malossi 19mm carb to solve engine overheating issue with BBK, not solved yet, still working on that one.
The OEM bystarter (choke) and auto petcock are pretty lame IOM and never had them work very well for me. I like the pod airfilters and have them on all my scooters. To choke the carb, I use a plastic grocery bag to cover the pod airfilter to seal it off, and kick it a few times and it will fire off. The grocery bag increases vacuum to the auto petcock which allows fuel to flow to the carb. Once the carb bowl is full of fuel, the engine will start right up.
The above is not for everyone, but works OK for me. Plastic grocery bag for choke is a very cheap manual choke lol's. Also, before I installed the pod airfilter on the People, I would stuff a plastic bag into the OEM air intake to choke the engine. The OEM air intake on Super 9's are not easy to access, but People was very easy to get to. I don't know about Like 50?
The Malossi 19mm carb comes with a remote manual choke. I didn't like it, couldn't figure out where to mount the remote lever and cable. I replaced the remote choke with the pull manual choke and really like it, small and simple to operate. Best of all, works very well. I think the BBK has sufficient vacuum so the OEM auto petcock works well. My People 50 2T with the BBK and Malossi 19mm carb almost always starts 1st kick.
After I get 19mm carb figured out with BBK, my plan is to install one on 49cc Super 9 LC, but haven't done that yet. I think it would work really well on 49cc engine with Tecnigas Trek pipe. Cheers