I damaged some Classic 200 when I built my first tubes. On those I had the film totally enclosed by the tube and that made it difficult to remove the film. Since I built my tubes so that the film extends past the end of the tube and extends into the cap I have not damaged a single sheet of film. I also use screen on the base side of the film to allow presoak water to access the anti halation layer. The screen also aids in removing the film since it allows some of the tension that would be totally absorbed by the film to be transferred into the screen. I just put the two substances (film and screen) between my forefinger and thumb and slide it out of the tube.
In regards to your pin holes, that could be due to a variety of things. The one that I have heard addressed fairly regularly awhile back was due to using a full strength stop bath. The reaction of the acid to the alkali in the developer can cause this to happen. The other thing would be dust in the holders (would prevent exposure of a spot on the film).
When I tray developed film I regularly exposed back up negatives. Since I have begun tube developing I have found that I don't need to do that any longer since my film damage problems have absolutely stopped at this point. This represents a big savings in film costs.