Co-Founder, Co-founder, or cofounder?
All are acceptable, so you should follow your judgement.
British usage generally favours rather more hyphens than American usage; I'd use co-founder since cofounder doesn't look all that natural. I'd omit the hyphen in landowner, though, so it depends.
Longman and Collins tend to prefer unhyphenated while Chambers, predictably, insists on the hyphenated form.
If you're using the word in a title (in which you can capitalize every important word) or at the beginning of a sentence, you should always use Co-founder, not Co-Founder; such as:
The Importance of the Co-founder in Contemporary America
For all other usages, just use co-founder.
Co-founder. Once hyphenated, the word is a single word, so only needs a capital at the beginning of the entire word. If you write Co Founder (which isn't really a word) then you'd capitalize both. co-founder works in a sentence when it's not part of someone's title. So:
Sentence: Elizabeth is the co-founder of the company. Title: Elizabeth Jones, Co-founder
[IMHO and American experience/prior and very ancient education]
Is it an actual title of address, like someone would be called, "Co-Founder Jones" in the same sense that someone would be called "Mayor Jones"?
If not, if it's simply the name of a job or role, like "engineer" or "accountant", then it is not capitalized. You write, "Bob is one of our co-founders," not "Bob is one of our Co-Founders".
If it really is a title of address, then it should be capitalized when and only when used as a title before the person's name. Thus, "The meeting was chaired by Co-Founder Jones", but "The meeting was chaired by one of our co-founders". (Well, it would also be capitalized when used as the first word in a sentence, etc.)
If it is capitalized, whether you should write "Co-Founder" or "Co-founder" ... my gut instict is "Co-Founder", but I don't know of any authoritative source to back that up. There's something of an analogy that when you have two-word titles, both words are capitalized, like we write "Vice President Jones", not "Vice president Jones". I think a hyphenated title would follow similar logic, but as I say, I don't have any independent confirmation on that.