I have been making some various enhanced leaf type stuff- one project being a grain alcohol soak. however, I forgot about the caapi leaves and now they been soaking for around 120 days.

The fluid is very green and the leaves are breaking apart. I'm wondering if I've pulled too much unwanted stuff out or degraded alkaloids in some way.

What do you think I should do- filter and do an extraction via Gilbrans tek? Thoughts?;

I dont see a problem here at all. No degraded (i guess they are conserved ) alkaloids ,maybe some more plant fats pulled.
I would just filter the alcohol once or twice and enhance leaf with it.
How mutch % was the alcohol ?

Yes alcohol is a preservant the harmalas should be fine, you have pulled chlorophyll and other stuff. You can leave it in direct sunlight to break down the chlorophyll I wouldnt be worried about the rest.