1. Check that you reconnected your IAT sensor after you did your breather re-route.
2. Make sure your throttle plate is absolutely closed all the way when you reset your TPS. Search other posts on various ways of doing this. I use ECMSPY readings to tell me when the throttle plate has stopped moving, snap the throttle a few times and back the idle adjust out another 1/2 turn just to be sure, but you might want to pull your airbox bottom off so you can visually inspect and make sure it's closed for peace of mind.
3. Pull your headlight fuse while doing your TPS reset or other ECMSPY work to minimize battery drain while doing the adjustments.
4. Since you just changed exhaust, your bike may run a little quirky until you do a tune. To get in the ballpark initially, you might ask around here and find out if someone with a similar setup can send you their ECM files (especially if they live somewhere near you or at least the same altitude/climate), and then tune from there.
5. When your idle is slow to return to normal, that could indicate that you've simply got your idle set just a wee bit high. Try lowering it just slightly to see if that clears it up.