This is not a part of the world where you can always count on the seas and ferries to accommodate tight schedules. A few years ago, when traveling from Turkey to Greece, we learned that the ferry between Rhodes and Marmaris is the more reliable of the two. We were told that the Kos>Bodrum ferry is more affected by weather. Since we had a plane to catch, we opted for Marmaris>Rhodes.
Will you be in Greece for some time before this trip? If so, you could call the ferry operator a few days ahead and find out if the Kos-Bodrum ferry will run on the day you need it.
To be even more certain, you might plan your journey to arrive in Bodrum the day before your tour leaves, giving you an extra night in Bodrum and some insurance you won't miss the tour.
If, when you arrive in Kos to take that ferry, you learn that it is not running because of a last-minute cancellation, you might have time to ferry to Rhodes and take the ferry to Marmaris and find a bus to Bodrum.
Or you could skip all this, just go to Samos instead of Kos, and take a day trip to Ephesus. There will be at least one tour daily but if Ephesus is your goal (and I think it's a worthwhile one), I'd spend a couple of days on Samos just in case. We did this and it was great; the ferry trip, guided tour and visa were included in one price. I have not been to Pamukkale but have read mixed reviews on it.
OR ... you could take the ferry from Rhodes to Marmaris a few days early. Take the bus (1 1/2 hours) to Dalyan for 2 nights (take a riverboat trip, see the Lycean tombs carved into the cliffs, have a mud bath, see the sea turtle beach and hospital), then make your way to Bodrum (3 1/2 hours) and the tour.
Lots of options. Lots of amazing things to see.
