Most of your problems stem from attributes being in all uppercase. I used to let Tidy convert them all to their lowercase equivalents (it does this by default), but this ended up wreaking havoc on SVG attributes. SVG has lovely case-sensitive attributes like "viewBox", and "viewbox" or "VIEWBOX" don't work. So I had to hack Tidy into leaving attributes in whatever case they came in.
I made this change months ago, and no one complained thus far. I plan on taking a look into making Tidy convert uppercase attributes to lowercase, but leaving mixed-case attributes alone. Sounds simple, but if you've ever taken a look into Tidy source code, you'd quickly realize it's not, mostly because Tidy source is a horrible mess of unreadable spaghetti C code.
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