So, I guess you’ve seen this post then with the inverted pulley ?
I’m not sure you need a gear puller, but if you’ve ordered one anyway it won’t hurt. Do be careful with the thin lip end of the pulley, these are generally pressed on and come off quite easily.
Although you’re right to worry about moving the load point further down the stepper shaft, inverting the pulley is not going to significantly change the load point. The inner round face of the pulley sits on the shaft so the loads should still be applied approximately where the belt tension is centered.
As for filing the shaft, I would not do that, it will definitely weaken the shaft and make it more prone to a fracture failure later on (which is a known issue).