When using elevated rails with the mod the later stages for some reason remove some of the elevated rails and need to be fixed also the elevated rail signals are fully out of place (on the ground instead of in the air) here are the screenshots of before and after a new stage
before: https://prnt.sc/Ph3t8L87iAqm
after: https://prnt.sc/0fvn1sUjq4Gf

Yikes, I thought I fixed this!
This probably needs an explicit build order for elevated rails; e.g. foundations first, rails next, signals last.

Yeah I think that would fix it because the elevated rail signals look like they're in the right place but are just on the ground.

Yep, turns out there's a whole as of yet undocumented api with elevated rails and rail signals.

elevated rails should be fixed in v2.8.6!

Thank you so much!