I did think some of the countries in MNM are redundant or unnecessary, so removing some of them's pro'lly a good idea, 'specially if the makers are asking you not to use it. Things where the culture doesn't already have a tag, or where the tag is far off geographically, I think add to the game though. Having Estonian nationalists without a tag to go to sucked (and having Welsh ones wasn't great either). There's a lot of double-ups for cultures that already have tags and a fair number of redundant formables, though. If you want my input, I'd say keep anything representing a culture, cut the others (also keep Iceland).
For reference purposes, my patch restored:
Where the brackets show what provinces they got cores on (some of them in historical dates and not the start).
Wales (241, 242)
Normandy (167, 168, 177)
Syria (1849, 1855, 377, 378, 379, 380, 381, 382, 406, 407)
The religious icons, in 0.55.1 at least, are all misplaced. The Catholics keep the right icon, but the Sunnis use the Hindu icon and the Orthodox, the Reformed icon, Shia's got the Taoist (vanilla Confucian) icon, plenty of other mismatches, and a whole bunch have blank space. You didn't include an icon_religion file, so the mod uses the default image, and since you've added new religions, things no longer line up numerically. e.g., Orthodox used to be religion #4, but now it's religion #3, so it uses the third icon. Maybe you just forgot to package icon_religion? Like you say though, you have icons from DG for 0.55.2 anyway, which should fix things right up.