Chris,
First a disclaimer. I am no expert but since you are new to body work also perhaps my experience will help you. I took a semester course at a nearby community college in autobody and I would guess the mistake you made was using power sanders on the bondo (filler). I know others with more experience will chime in but I believe you should use block sanding by hand, approaching the area at different angles. I think that allows the block to use the surrounding normal metal to act as a guide, as you sand.
For the course, I worked on my COE fenders, which had a few significant dents as well as marks from a chain that had penetrated the fender ( I think they were trying to pull the truck with a chain around the front axle and the chain broke). After much hammer and dolly work, combined with welding the perforation closed followed by heat shrinkage, I used a thin skim of filler and block sanded. You absoluteley cannot see any of my repairs after it was painted, so I know if you block sand it, you will be pleased, as well. If I can do it, so can you! Now painting, that is a different story.
Regarding the change in texture where you wore through the putty, I would think if you primed and sanded the primer properly, you wouldn't see that. Perhaps you needed to use a high build primer.
Kent
