Wayne, if you don't size all the way down you can push brass down and bulge the bases, and that is what you are seeing on the cases you had problems with. If you size all the way down it will still push the brass down and bulge out, but when you get close to the bottom of the stroke the brass has nowhere to go and it will have to spring up into the die. When it does this it will be sized and the bulge will be gone. With the price of 9mm brass I would not worry about roll sizing or anything like that. Size down as low as you can. Load them up and if they don't fit pull them down and throw that case away, re-use the rest of the components.
I don't know if you need a custom seating stem, but you can probably find one that fits the bullet a little better. Easier still and a lot cheaper is to use up the bullets you have and buy different bullets that fit the equipment you have. "Less" pointy is what you need to look for, then the seating stem will have a better chance of seating them straight. If the bullet fits the seating stem well you can have a significant angle on the bullet as it starts into the die to be seated and it will seat straight.
I think this has been a 'good' problem, lots of experience troubleshooting problems and things that will stick in your mind if you should have problems in the future. Most of us started reloading before the internet forums were available or used by us, and unless you had a skilled mentor problems were solved by persistance alone sometimes. Forums like this sure are nice, several guys with dozens of years of experience have seen most of what can go wrong between them.
Good job on figuring it out and getting it working!!!