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So after struggling with Jak and Daxter for way too long i've found that i have to choose between working eyes in software mode, or working shadows with skipdraw.

Is there a way to turn skipdraw on in software mode? because then the shadows would work and i can actually play the game

Nope.
Skipdraw is a hardware hack only.

so there's no way to get jak and daxter eye fixes and shadow fixes to work in tandem?

You'll have to go with shadows if you want to get the jumps right.