There are a lot of things here...
1.) I wasn't aware Termignoni made an exhaust for the XB. Did you get a corresponding map for the exhaust or did you just run as is?
2.) When you got the pump (I assume full assembly?) did you check the plastic hose that connects the pump to the regulator for any leaks? Over time the plastic gets brittle and if there is a small leak there, your pump will be constantly working hard to maintain pressure in the line.
3.) TPS could be the sensor on its way out. I had something similar with my bike (09' xb12s) when I purchased it used (would not hold idle, would start fluctuating and then cough out unless throttle was applied but ran better when warmed up. Turned out to be a bad TPS sensor) but as others here will chime in, there are a lot of things to check, so wait on throwing parts at it. File it away as a possible issue.
4.) Bank angle sensor... make sure everything is plugged in under the seat. It is possible your mechanic unplugged stuff while working on the bike and didn't put everything back together again.
5.) IAC... this can be cleaned relatively easily to check if it is dirty and gummed up (info can be found via google)
6.) Jacob Stark and various other people here on the forums and FB page are good resources to further diagnose the source of your problems, but there are a few of the items that pop up to the top of my head.