You need to do something to remove all the rust inside the tank or it will be a continuing problem with plugging up the fuel filter. There are several ways to do this and several systems on the market to do it, a search should come with plenty of options. You might need to replace the filter again after you're done with this.
The TPS needs to be adjusted. My experience was that most bikes when new were off. You should also balance the throttle bodies while you're at it. The proper order is adjust TPS, balance TBs, adjust YPS. The two together makes a huge difference in how the bike runs. And finally, IIRC the Power Commander requires that you calibrate it to the throttle, at least the version I had did. How to do that was in the instructions. If you don't have them they are probably online somewhere or someone here can tell you how to do it.