Not sure I fully grasp what you're getting at when you say (re square bobbins) "drill them to suit the size of the magnet" nor how could this proposale "reduce the height" .....I'm all ears, could you put more meat on the bone?
I may have misunderstood, but I thought you said that the magnets were different sizes which was causing problems with holding them? If you use a square bobbin then it could easily be shaped to suit the magnet size (or epoxy the smaller ones)

I was thinking of the small plastic box section that you get from model shops, if you cut to size and put a small bolt through with a washer on each end then you would have a former and be able to hold it in jacobs chuck......

With regards to reducing height I meant that if the square section utilised the availble space better then it wouldnt have to be as tall...

Is that better?