I am thinking to avoid this problem again, I should avoid a liner and
go with a plastic spillway. Since I need to retrofit it into my
structure, I don't think any of the pre-formed ones will fit properly.
Has anyone made a homemade one?

I haven't. However, if you are handy, you should be able to shape PVC
or some other cheap plastic sheet (hint: local plastics supply)
with a heat gun quite easily. Be sure to look up safe handling of
heated plastics before you try. Better yet, ask the plastic supply
guys; they'll know.

C//