In my view, you don't NEED a power commander or a remap. Ensure you've got the correct EPROM fitted (DP08054/11) get the balance and CO set up correctly and I guarantee that if there isn't air leaks or some other underlying problem it will run very well! One other thing - TPS value on 996 should be 423 mvolt
If it's just had new slip ons, chances are it's an air leak. Slip them off, use some combined lubricant/sealing paste (Firegum?) to slip them back on again.
It's not uncommon to have pops from the exhaust on overrun after fitting less restricted/ baffled silencers on carbed and efi bikes.
Agree with Rman. Get it set up properly with a decent EPROM first. I've seen loads of power commanders sold and tuned to sort issues out that could have been sorted with a decent tune.
Is it the 1.6m ecu? My old 748R did exactly as you describe. I enriched it up as below and it was good as gold...
I have one sat here amongst my spares from my 996. If CR is interested I'm up for selling. Also have a set of sps cams that would go in nicely ;-)
So you just turned it up a bit? Did you actually set to a level and measure or just turn it a little bit and try it?