You should thin down the shaft if you are keeping the stock bore, big gains to be had there.
To remove the shaft:
Remove tb plate screws, 2-t20 torx then pull out plate. Be careful, because the screws are weak, and the heads tend to break off. Once the plate is out scribe a line where the shaft meets the bore on both sides.
The nut needs to be removed on the linkge side. then remove the linkage. Remove the TPS sensor on the other side.
Tap lightly on the shaft from the linkage side to pop it out the tps side. The shaft is interference fit to the bearing on the linkage side. The shaft will force out the bearing and retainer on the TPS side. You may need a punch to follow the shaft out as you do this. The pin in the TPS side can be removed by using a hammer, resting the shaft on a piece of wood, then following it out with a punch, then twisting it out with pliers.
The bearing and retainer will now slide off the shaft.
You can now thin down the shaft by sanding it dow, it goes pretty easy, as the metal is fairly soft, just don't go beyond the lines you scribed before removing the shaft.
To reinstall the shaft:
You'll need to pop out the linkage side bearing, to do this put the shaft back in and tap on the other side with a hammer, this should pop out the bearing. You'll need to install that bearing onto the shaft, first, then install the shaft/bearing from the linkage side.
Keep in mind the shaft ends may have mushroomed a bit from hammering on them. You'll need to sand them down a bit to fit the bearings over the ends.
Use a long socket as to not contact the shaft and tap the bearing/retainer in the linkage side, then slide the bearing/retainer on the TPS side and use the socket method to fit the bearing back in. Then put back in the pin at the end of the shaft. Done.
And yes the LT's will be off a bit. More air = the need for more gas, if the LT's are more than 10%, then you'll need to mini-afc it, but you should do that anyway.