Well thank you for bringing these issues to attention. I have corrected the banner issue and instated the pagan style banners for the Western empire. As for anything else you mentioned such as for ships and character portraits those simply couldn't be changed due to a variety of reasons.

A bunch of issues with this mod need fixing.

It seems that this mod is somehow the More Historical Vanilla Roman Reskin mod, and not the More Historical Vanilla Roman Reskin (Pagan West Only Version).
As an example even though it is supposed to be WRE only, the ERE is also being affected by this mod.
Character portraits are identical with the More Historical Vanilla Roman Reskin mod for both WRE and ERE
Crosses still appear on ships as well as other symbols.
Ground units mostly carry Chi ro's or golden dog heads as their standard.
Both WRE and ERE armies on the campaign map appear as pagan even though for this particular mod the east should remain christian.
There is probably more but that is what i've noticed.

Awesome