Hey loosend,
Your bike is breathing better now so you probably are running lean. A lean mix makes for hard starting. That's why you have a choke to richen things up. You probably could help the situation some by turning the air mix screws out a bit. Turn them out counter clockwise (richer) a quarter turn at a time and take a ride to see if it helps. The best thing to do is to turn them all the way in until they just hit bottom, not too tight though, don't damage them. Take note of how many turns it took to bottom out so you know where you were before you started adjusting. It should have been about 3 turns +/- 1/2. Turn them back out the same plus 1/4, or about 3 turns, which ever seems right. (This is seat of the pants stuff, not Sigma 6) The book says three turns. Make adjustments from there. Keep in mind though that the air-mix screws (and pilot jets) affect mostly the low end when you are just above idle or coming off throttle and decelerating. Air mix adjust and pilot jets have some but very little effect on the mid to high range.
A better solution is to re-jet. It sounds daunting, but it's not that bad, and it really helps you learn your way around your bike. The worst part is getting the airbox separated from the carbs. There are two hex screws under the rear fender that need to come loose. Dinqua has a great howto with pictures posted on his website. I'll put the link below, or you can find Dinqua's user profile and click on his homepage. He has gone to a lot of work to post some great information.
Your bike probably came from the factory with 120 main jets and 42 pilot jets. Going up to a 45 pilot jet might help both starting and popping on decel. Bigger main jets would help your top end (4500+ rpms).
My pipes are Staintunes, which are straight through absorber types with no baffles. I can see right through them like a telescope. I first tried 45 pilots and 135 mains and was fairly happy with that. I've tried several combinations and right now I'm running 45 pilots and 138 mains. Seems pretty good there.
Oh, by the way, I'm at about 800 ft in elevation. The higher you go the smaller the jets you need.
Hope this helps some.
John
Dinqua's "Everything you want to know about working on a Triumph" site