The current panel stair model creates a minor inconsistency in how stairs, slabs, and planks interact when used in combination, which causes them to stand out a bit:

An example of how it looks in vanilla:

Ah. I've just realized that an issue exists for this already (issue #8). My apologies.

Yup
This has been there since the beginning, might need to change the way panels look to fix it properly
Probably needs to be a horizontally rotatable planks block turned on it's side x)

Here, I fixed it

This is a resourcepack that edits the three template files for the stair blockmodels; I don't know how pull requests work or if I can even create one, but feel free to use it in the mod, if possible.
ilikewood-stairfix.zip

Does it work if you turn the stairs upside down though

Yep. The first screenshot demonstrates all stair variants in action
Edit to add a screenshot showing the upside-down stairs working

still doesnt line up on some rotations properly x) I will have a look at it when I am doing with what I am working on atm

Seems I didn't realize the scope of the problem: Apparently it's an issue with Minecraft's stair block implementation (or possibly general rotations...); evidently it doesn't really like rotated UVs. I wish you the best of luck on coming up with a good solution.
It's kinda weird that it doesn't have a problem with upside-down stairs, it just specifically breaks the uv orientation for regular stairs, despite using the exact same blockmodel...