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So modern period would start with 1000, crypt era at 2000 and GFL era at 3000.

Rookie 3000, Starter 3200, All Pro 3400 . Then if you have a story to be read between Rookie and Starter, you drop it into the middle of the range at 3100. Then if that had a follow up story you would subdivide again and it would be numbered as 3150. 

Doing this gives it simple sequence with a lot of gaps to be filled.

I'd also add the suggested three letter code for the series after the number, so the sets can be identified on a shelf ( e.g. 3200-GFL )