All Shikoku + Okayama, Hiroshima, Yamaguchi

My intention is to fly into Kochi and use the JR All Shikoku Pass for 3 days and then get to Okayama and use the JR West's Okayama, Hiroshima, Yamaguchi Area Pass for 5 days and then fly out of FUK.

I will be exchanging the passes at JR Kochi and JR Okayama, respectively. Based on what I've gathered, I can take a Ltd Exp. Marine Liner from Takamatsu to Okayama. The Shikoku Pass will only get me to JR Kojima. Should I ask for a ticket from Kojima to Okayama at JR Takamatsu so when I alight at JR Okayama and head for the ticket office to get my pass from JR West I can show the attendant at the manned gate the ticket for the portion not covered by the JR Shikoku Pass? Or can I also use the manned gate for the fare adjustment from Kojima to Okayama instead of getting a ticket at Takamatsu? Or can I get the fare adjustment from the conductor on the Marine Liner as we travel to Okayama?

I travel a lot in Japan, but this is the first time I would run into a situation such as this that would warrant me asking such a question. Thanks!

I would do option #1.
I think option #2 would be slightly more difficult and I can't remember the ticket checking process on that train (a couple of years since I last used it).
On the few occasions where I am entitled to a pass and then go outside the coverage area I work on the basis that I have a valid ticket for each part of the journey before I get on the train. I have only done this a few times and it seems to work ok.
As you note, in your case, you are covered for the first part of the journey, including across the bridge, but not the last bit up to Okayama (fortunately only Y1,000 on the Marine Liner).
(If you were flying via Kansai you could get the JRWest pass there as it covers to/from Takamatsu, but I guess you are not otherwise you would be doing that already.)

Why not do the trip in reverse? Start at Fukuoka so you can exchange your pass at Hakata, and then you'll be covered until Takamatsu. Where you can change for your Skikoku pass at Takamatsu.

@JapanCustomTours, thanks, I think I'll go with option #1 when the time comes. It's better to be prepared than to stumble after the fact.

@Hakata14, thank you for the suggestion. It'd work perfectly. But I'm someone who likes to fly into new places and FUK isn't one of them! KCZ would be! I have an odd interest in luggage tags.

All Shikoku Rail Pass =3 days=9000‰~
JR Okayama, Hiroshima Yamaguchi Area Pass=five days =14500‰~
Total cost=23500‰~
I suggest you to buy Japan Rail Pass= 7 days=29110‰~.This will give you peace of Mind.

One More Thing:If you want travel like Me,Then I can give you idea on My personal experience.After Landing Japan,I bought JR Nationwide pass From Kansai intl Airport.In My case,Money is not the problem.I came here For Travel As much as possible.I want to see,How Japan Looks Like.How they Build their country after WW2.So on My First Day I went Kansai intl Airport to Kagoshima and Back.On My second Day I went Shin Osaka to Sapporo.So if You are young generation,Your First priority will be Travel As much as possible.But My Dad and Mom Dont like cross country travel.So they most time stay in Hotel,go to onsen,Dine in a local restaurant and Hangout with their countrymen and travel a bit with local pass.

Thank you @jack for your recommendation, but I don't need the national pass. Plus, I gain a day more for about 5500yen less, which turns out to be a night's lodging cost in most of the Toyoko Inns.

I've done quite a bit of train travel through Japan and once (2015) I flew to FUK to start my 21 day JR pass and went to Kagoshima, Kumamoto, Nagasaki, Fukuoka, Hiroshima, Matsuyama, Uwajima, Okayama, Matsue, Himeji, Kobe, Kyoto, Kanazawa, Kesennuma, Aomori, Hakodate and Sapporo before flying back to Haneda. It was a reconnaissance trip to gauge my interest in each city and if I'd like to return to them in the future. I've hit 41 of the prefectures so far and I return to those places that interest me on future trips to spend a little more time in each.

I forgot to mention the prices are reduced if purchased in advance: 8500+13500=22,000 yen versus 29,000. It's a savings of 7,000yen with one more day of use. :-)