If the only change has been the can, you wouldn't think that "bogging down" would be the issue. If anything, a more open exhaust should cause you to run lean. Might just be an adjustment issue. Or maybe a previous owner has already monkeyed with the carbs?
Although these CV carbs have limited upside, there are a couple of mods out there that can give you better/quicker throttle response. I'm no expert, but I've done one of them (the tunebike carb mod), and it did help. Now the response on mine is noticeably better than stock.
Give them a try:
http://www.tunebike.deActually, I think it's not so much changing the jets that helps. it's the spacer/venturi tube mod to the primary carb that seems to make the most difference. Changing secondary main-jet sizes should only be done to compensate for a freer header/exhaust can. I've heard that some guys just do the primary carb/spacer thingy and leave the jets alone and still get good results.
These guys sell another carb kit for the Baggy/Mastiff that is essentially the same (I think Dynojet supplies the parts for them):
http://www.off-the-road.de/vergaser_vergaserkits.html?&L=1Good luck!