I guess that's progress? The MD5 is the same so the zip should be correct, but it still sounds like something is very wrong with the setup. Now that we're known good at this point it might almost pay to do a completely clean reinstall: delete everything that's on the Vita and install the 4.0 vpk, and then overwrite the Media folder with the unzipped Media.zip./
Frankly I'm impressed that you've stuck at trying to figure this out instead of bugging someone on reddit/discord for a working copy lol