I ran through the map, looked at all the items I had in chests and it seems that everything is fine except for the mage NPC which is still not retextured for some reason:
View attachment 272624
As for the 1.4.0.3, notes says "Added a large quantity of art asset revisions, mostly minor touch ups, but several with substantial changes, most notably, the Molten weapons and tools, Clentaminator, and S.D.M.G." Aside from the mentioned items I have no idea how you would find the items that changed and just thinking about it gives me a headache.
About the install method, I like the "ResourcePacks" folder method, it's a lot simpler and more intuitive, it would just be nice if you gave instructions about where to install it on the readme file, lots of people don't know about the new method of installing texture packs.
Now if you don't mind, how exactly are you managing to work on this mod? Long ago I was trying to do precisely the same thing myself but didn't manage to find a 'batch XBR/XBRZ filter applier', and the thought of changing every single texture one by one made me abandon the project, I wish a software like Gigapixel existed for this kind of filter so I could just drag thousands of textures at the same time and just leave it there for half an hour and BAM! Done!
Anyway, once again, I really appreciate the work you've been doing man, keep it up.