During the removal, if it won't budge, just leave tension on it with the puller and let it sit overnight. Most of the time you can creep off the really stubborn ones.
Also, use grade 8 bolts of the proper size, run a tap down the threads in the rotor to clean them out and use a proper length bolt so you get full thread engagement.
Then, after you remove it check the shaft and the bottom of the rotor for any nick, burrs, or deformation. Check to see if the end of the shaft has been mushroomed. If it has, grab a file and put a slight chamfer all the way around the top edge.
And the biggest piece of advice, if you start getting frustrated, just take a break.