Here are my thoughts...
All of my females are morph females, 3-4 of them, his male is a double codom. It takes me way more time to raise the females to breeding size than it did for his male. In fact the females are of equal or more value (genetically speaking) to the male. Wouldn't that mean I would be better off buying my own breeder male?

You answered your own question, yes you should own your own males, for so many reasons.

It can be anything you work out. You are right, it isn't fair to split 50/50, unless the males were special. If the males are VERY special, they might deserve more. All the things you mentioned are true. Talk it over with your friend, neither of you should be worried that your breeder loan isn't in my favor as much as so and so said I should get.

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