Does anyone have any linkage information on how the McCracken's are tied to the MacNaughtan Scottish clans?

There is a Clan McCracken International organization. Contact TMcCraken@email.msn.com. Perhaps this person can explain the reason why the McNaughton clan includes McCrackens

My great uncle (Alex Mcracken) married Grace
McNaughton. I am just starting to fill in the
blanks on my tree. I would like to hear more
on your side.

I have a document that shows the changes in the name from Mac Naughten to McCracken. This was done by my father's cousin, Eugene McCracken of South Carolina around the mid-1970's. Here is a summary:
Original Spelling -- Mac Nachten --- Mac Naughten - modern spelling --- pronounced Mac Rachten -- Gaelic origin
Then the "T" was dropped --- Mac Rachen.
Then the "c" sound was duplicated -- Mac Crachen.
Then the "ch" sound spelled with a "k" -- Mac Cracken.
Then the "mac" was abbreviated -- Mc Cracken.
Then the two words joined together -- McCracken.
I have more paragraphs to write about this and will put it in another response. Take care.

Yes, I would also like to know how they are related. I have some photos of my Scottish ancestors, even the venezuelan ID card from late 19th century of my father´s scottish grandpa who emigrated to Trinidad. Don´t know when, why or how, we even have some furniture they brought with them in the ship, some Thonet old chairs and sofas, my grandparents, my parents and other relatives, signed their civil marriage documents sitted on those chairs ....it´s a family classic !!!!!

I've seen the same analysis that you're getting from others here and it's a bit weak for my tastes. I'd love to see something other than 19th century linguistics (which may be accurate but are not definitive). An actual connection would be more convincing, for instance.

The MacLean clan also counts MacCracken as a sept, so it matters perhaps where your ancestors came from. Mull is probably closer to MacLean, but Lewis or Argyle might mean your ancestors were closer to the MacNaughtans.

I have a 1970's document passed down to me from a cousin of my father who lived in Savannah Georgia, his name was Eugene McCracken - it is several pages but I have only included a few paragraphs in this email.

The last page of the document includes the contact information for the Clan MacNachten Association in the United States - James W. McCracken, President -- 3150 Callecita, Sacramento, CA 95815. And this name appears at the end as well -- Philip D. Smith, Jr. PhD -- Fellow of the Society of Antiquaries of Scotland - Wrote a book called, Tartan for me! It is a book of Scottish names. He was professor of linguistics, and he taught Scottish Gaelic and wrote about Scottish and Scottish-American culture. Keep in mind this was created in the 1970's.

So here goes:

Gaelic, like all languages, has its own special sound and spelling rules. These are not just 'made up' but have reasons. Fore example, it is physically difficult to make a /k/ sound at the back of the mouth followed by an /n/ sound at the front of the mouth. In English this has resulted in the 'silent' /n/ in the words like 'know' and 'knot' where the /kn/ combination used to be fully pronounced.

Gaelic speakers had a different solution to the very same problem. Over time they developed the habit of pronouncing the /kn/ combination as if it were /kr/. Gaelic has not letter 'k', and the /k/ sound is spelled with a 'c'. The word 'cnoc', 'hill' is pronounced like the English word 'crock'; 'cno', 'nut', like English 'crow'.

This rule, that 'n' after 'c' is pronounced as 'r', applies to names beginning with 'n' when the word for 'son', 'mac' is put in front of them. 'Neil' is a personal name. The 'son of Neil' is 'MacNeil', pronouced /mak reel/, because the 'n' of 'Neil' now follows the 'c' of 'mac. The name MacNichol' is pronounced 'Mac Rickle'. The name 'MacNaughten' is pronounced like 'Mac Rackten' in Gaelic.

This was how the "MacNaughten" pronounced their name when some of the family moved further south into the area of Scotland called Galloway. Here the Scottish dialect of the English language predominated. The Gallwegians, hearing the Gaelic pronounciation of "MacNaughten" with an "r" in it, called the new people the "Mac Racktens". In time the "c" of "Mac" crept over and the "t" disappeared in rapid speech. The name became "Mac Cracken". "Mc" is an abbreviation of "mac" common in both Scotland and Ireland. Here is the progression from "Mac Naughten" to "McCracken"

Original: Nachten Personal name
Mac Nachten Mac Naughten (modern spelling)
Mac Rachten pronounced
Mac Rachen /t/ dropped
Mac Crachen /c/ sound duplicated
Mac Cracken /ch/ sound spelled with a "k"
Mc Cracken 'mac' abreviated
McCracken two words joined