TEHRAN - Gary Sick, a U.S. academic and analyst of Middle East affairs who served on the U.S. National Security Council, says a report by the BBC Persian that Ayatollah Khomeini relayed messages to President Jimmy Carter before the victory of the Islamic Revolution in 1979 is riddled with “factual errors”. 

Using newly declassified U.S. government documents, the BBC Persian on June 3 claimed that Ayatollah Khomeini sent a secret message to Carter on January 27, 1979, asking him to use his influence on the Iranian Army under Shah to avoid military coup and instead promised to calm the Iranian nation and protect American interests and citizens in Iran. 

The BBC also claimed that Ibrahim Yazdi, who became the first Iranian foreign minister after the revolution, was named as one of Ayatollah Khomeini’s contact persons.  

However, Yazdi has rejected the report, saying the one who first sent a message was President Carter not Ayatollah Khomeini. Secondly, he said, the exchange of these messages for the first time was done by Gary Sick as asserted in his book “All Fall Down”.

The BBC also claimed that Ayatollah Khomeini had similar contacts with President Kennedy in 1963.

Following is the answer provided by Gary Sick to the Tehran Times about the “authenticity” of the BBC report: 

I wrote at length about these contacts in my book All Fall Down (Random House 1985), pp 140-147. My account was drawn directly from the documents that have now been released and I quoted many of the key phrases that the BBC has identified, plus others that are equally important but not mentioned in the BBC report. Regrettably, I do not have the text of the book in digital form, but it is available in paper for anyone who wants to look.
Here are some comments about specific aspects of these exchanges that may cast some light:
First, these discussions between Warren Zimmermann of the U.S. Embassy in Paris and Ibrahim Yazdi, then a close aide to Ayatollah Khomeini,  in a small inn near Neuphle-le-Chateau were discussed in advance with the shah, who encouraged the contact in order to avoid bloodshed in the wake of his departure, and with Shapour Bakhtiar, the shah's nominee as prime minister. 
Second, these contacts were essentially a negotiation about the role of the Iranian military and constitutional procedures after the shah's departure. The U.S. wanted to preserve the military as an institution, while the Khomeini forces were concerned about a possible military coup. Both sides wanted to avoid a collapse of order and a possible bloodbath. The discussions were essentially inconclusive and ultimately had little effect on the course of events.
Nobody in the U.S. government (nor in Iran, as far as I know) interpreted Khomeini's words in these messages -- or in his public pronouncements in favor of peace, stability, democracy, human rights, women's rights etc. -- as evidence that he either wanted or expected a continued close relationship with the United States. 
Finally, I have no knowledge of the reputed message from Khomeini to Kennedy in 1963, and it is very evident that nothing came of it.
Apart from selective quotations, there are some factual errors in the BBC report. For example, they claim that "On 9 November 1978, in a now-famous cable, "Thinking the Unthinkable," the U.S. ambassador to Iran, William Sullivan, warned that the Shah was doomed. He argued that Washington should get the Shah and his top generals out of Iran, and then make a deal between junior commanders and Khomeini." The message was actually on Nov 2, it did NOT claim that the shah was doomed, and the deal that was eventually worked out by Sullivan with the Iranian opposition was done without Washington's knowledge or approval. There was certainly no mention of such a deal in the Nov 2 cable.
Basically, this is a tempest in a teapot. The details of the exchange, in their full context, have been available in the public domain for at least three decades. The release of these documents, while welcome, adds nothing that we did not already know.