"The other reason she liked this path was that she seemed to be the only pony whoever used it."

What I've always learned is that in this case, it should be written as 'who ever.' This has been something that bothers me, and I have gotten conflicting answers every time I've asked. So I figured I'd give it another go here. Thanks for the help!
"Whoever" as a pronoun is one word meaning "whatever person, or anyone that, or no matter who." However, in this example, "who" and "ever" are distinct words. This is obvious since "ever" is being used to mean "at all times, or at any time" in this context. As such they should be two words.

As an aside, personally I would use "that" instead of "who" when referring to a pony.
Who ever used it = Who [person just referred to (in your example) ] ever used [adverb and verb] it

Whoever used it =Whoever [person unknown, not referred to] used [verb] it

He was the first man who ever ran a mile in under a five minutes
Whoever ran a mile in under five minutes should come here for an award.

Who ever ran a mile in under a minute? (ie no one)

Pony should normally be 'which ever' and 'whichever'.

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Thank you for clearing that up! Also, in response to your aside; the sentence is from an MLP:FiM fanfiction. So that's the reasoning behind that bit of wording.
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MidnightSpark, you are correct.
Whoever is a pronoun meaning "a person who."
"Who ever" is a pronoun plus an adverb.
Totally different meanings.