Specifically, towards the interview's end, this wild claim is advanced:
First of all, one of my two biggest discoveries that I made in the two years that I have been researching this birth certificate controversy has nothing to do with the birth certificate. It was discovering that Politifact had started the false rumor that Obama's middle name is Muhammed, and used it to endlessly "debunk" it in conjuction with facts about Obama.
This is a rather specific allegation, and since it's called a "discovery," that implies there's some kind of evidence to support it. (As opposed to it being just random speculation.) But no supporting evidence is identified; just the conclusion.
In fact, and contrary to the claim as made, the "Obama's middle name is Muhammed' rumor did not originate with Politifact. As far as I can tell, it started with this e-mail forward in December 2007. It started hitting a lot of websites in early January 2008 (for instance, it was posted at FreeRepublic on January 4), and got relatively major exposure via Bill Cunningham on January 6.
Politifact did indeed move to debunk the rumor quickly, but their article about it came on January 11, 2008, five days after Cunningham's usage on the radio, and nearly three weeks after the e-mail forward that was submitted to About.com.
So unless the allegation is that Politifact created the email forward in mid-December 2007, filling it with talk about Trinity Church, and using it to introduce a fake rumor that it would then shoot down a month later, this conspiracy theory simply has no legs to stand on.
And if the allegation IS that Politifact secretly created an email rumor about a Presidential candidate just to debunk it a month later, well, it's hard to imagine what secret evidence could have possibly been "discovered" to validate such a hypothesis.