I've looked it up, and I'll keep looking, but thus far, I've seen nothing that would indicate that Goldwater didn't write The Conscience of a Conservative (with Bozell assisting, of course, but not writing the whole thing himself).
Also, don't forget that Barry Goldwater endorsed Gerald Ford over Ronald Reagan in the 1976 primaries and endorsed Bill Clinton over Bob Dole in 1996.
Where are you getting your information? Goldwater was appalled by Nixon's handling of Watergate and called him "the most dishonest man I've ever met," so I'm not sure he'd have endorsed the man who pardoned Nixon. And I know for a fact that he actively endorsed Bob Dole. He was considered controversial in the Clinton years for his support of the "don't ask, don't tell" policy, saying that he couldn't see a reason why being gay would intrinsically hurt another.