From what I've read here, the hot tube is the most restrictive thing in the exhaust system... silencers don't add or subtract much flowability, but removing the hot tube is one of the only ways to give more breathability. I removed my hot tube, installed a K&N filter (open to the air) and experimented with jets and needle settings and the mixture screw.
I have the BS29, so my settings won't be relevant to yours, and I also think I'm running a little rich. From what I understand, the low end torque is based on a combination of the air/fuel mixture screw and the needle height- main jet doesn't come into play until higher throttle ranges. When I removed the hot pipe and went to a glasspack muffler like yours I also had some similar symptoms of starved throttle ranges, and it took some experimentation to get it to a workable setting.
I have the BS29 and a 17.5 pilot, 122.5 main (probably too rich), and my needle is at the richest setting then raised even more by a tiny washer (shimmed it up). Idle mixture screw is 1/2 turn out. I think the change that yielded me the most power was raising the needle height. When I removed the hot pipe and added the free flowing intake I needed to add more fuel into the mixture, and now that I've done that it has a lot more power than it ever had before.
Sorry for the rambling but I was bored. Hope this offers some help. It's a great bike without the free-flow mods, and it's a great bike after doing the mods. Takes some time to get it set up right, and it might not pull as smoothly as it did stock, but it'll have much more growl and power once it's done successfully.
Best of luck!