I don't think the mpq files are case sensitive, I test all my model swaps using lowercase and they seem to work for me.
I also finished all the requested model swaps expect the druid flight form, you can Download them here:
[spoiler] Ironbound Proto Drake to Ony Mount
Red Dragonhawk to Ony Mount
Red Drake to Ony Mount
Red Proto Drake to Ony Mount [/spoiler]
Note: You have to rename the file to "patch-x.mpq" for it to work, the "x" can be any letter from A to Z or any number from 1 to 9, I'd strongly suggest using letters though. Seeing as Blizzard tends to use numbers when they patch.