Sixpack do you have tune boy? if so you can check some things out like TPS Setting especially the ISCV sync between the idle stepper motor and the Primary TPS. You should also check the throttle boddy balancing as it might need a slight adjustment. Als look at whether you hav the secondary throttle plates installed or if they have been pulled. A 12 minute tune will not hurt to do start the bike up do not touch the throttle. Let it idle until the fan kicks on. Once it does let her run 12 minutes to resync its self. Also if it has not been in the shop they had a idle tune modification they came out with in 07 for the bike. The decel popping could be from the Triumph Tors tune. I would reflash the ecu with another map even if it is the same map reflash it. Then 12 minute tune. If you do not want to sit around and watch for the bike fan to kick on start it up and walk away for minimum of 25 minutes 30 will insure the 12 minute tune is done including the warm up cycle.
Of course checking for vacuum leaks as suggested above will not hurt especially if it has been disturbed under the tank like if three K&N filters were installed.
Hope this helps let us know.