My bike had a similar problem and improved it by ajusting the idle to 1100 revs as per factory specs as when staintunes were installed it was idling slower so popped on the over run,Also my local bike mechanic tweaked some idling mixture screw on the underneath of the throttle bodies and balanced them so that popping has all but been eliminated except at very slow speeds.On my film clip on youtube when first installed you will notice a bit of popping which was a bit annoying but after throttle bodies balanced was 100 percent better so maybe need to check balance.It also used to hunt at low speed through towns but now almost but not entirely smooth .If in first gear up a mountain behind a slow truck is when it can be felt .My bike is on 20,000 klm no w and all seems well ,even the amber light issue is finnally sorted out so even if I accidently try and start while bike in gear ,the light will go out after 10secs or so. My bike was the very first to have Staintunes so factory used it to Dyno test and did not think it needed a power commander and to be honest quite happy now.
Hope puts your mind at ease.
Saw a V7 cafe in Italy while overseas that had mistral pipes and they sound more mellow and dont seem to boom as much as mine but I must admit that at about 110klm /ph and open up the throttle is when they sound the best
Enjoy your bike . Ian

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Thanks for the info about Charnwoods, I have brought from them before.
What I was after was your old fitttings, or pictures of them; as I have a large box of assorted fittings already
cheers
Andy

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