I have my new wideglide, VH slip ons, S&S AC and VH Fuel pack 3.
Ive downloaded the correct map, its been auto tuning for a week and runs pretty well...

But, im noticing as I approach a red light or brake hard for a corner when the revs are hitting 1800 or so its holding them, theres a slight surge (disconcerting coming into a corner) or even as you come to a stop at the lights the engine revs along ahppily at 1200rpm for a bit before slowly dropping to idle.

The other end of that, starting cold... terrible hesitation at really low rev settings, stumbles and stalls.

Any advice? I know one of the mufflers is leaking a tiny bit (some pops on decel) but I'm not sure thats the problem.

Cheers

can you compare the original map to the new one? look for significant differences

with the cold start, hesitation, stumble & stall look at IAC steps and bit more fuel

Had a similar problem with mine, ended up being the TPS had been damaged. Yours could just be the leaking exhaust so I would fix that first especially if u have been auto tuning with the leak. If so go back to the std map and fix the leak. Advice from V&H was to run at least 2 tanks of fuel after repairs b4 auto tuning again.

Assume u are running 98fuel?

well I reverted back to the standard "VH 3" slip on + Aircleaner map".. 
Didnt even think to do that, seems the auto tune had put the map so out of whack, bike seems much nicer now.. good thinking guys!