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There should be no clunk when switching from EV mode to ICE and back to EV. But, I doubt it is the transmission. It's more likely engine / transmission mounts or something in the front end suspension / cv joints / maybe steering. What are the inputs to the car when it happens? accelerating, decelerating, braking, uphill, downhill, coasting, cruising, low speed, high speed and so forth? How many miles on car? It sounds perhaps that when there is a change in torque requirements (whether in EV or ICE), you sometimes get a clunk (like one does when a CV joint has failed). Have you had the car serviced recently? If so what did they do?

I actually like Sync 2 a lot, having the interface laid out in quadrants and with some manual knobs and buttons is great. My only complaint is that the hardware seems underpowered - it takes too long for screen updates. Competitors products like Entune don't seem as polished. I tried using Sync 3 and hated it - it was faster but I found myself constantly having to look away from the road to read the screen and figure out what to push. I also spent 10 minutes trying to speak a nav destination in a different state.

Yeah Ford really dropped the ball with Sync 2.

There's a procedure for "re-training" the auto functions - read this thread. I've had to do some windows but not the roof so don't know if procedure is the same.

Yes, exactly the same files are included in my zip package once you open the folder.

No the Ford site stopped letting you download the releases so I downloaded it from someone on the internet. Here is the thread where I updated to 3.10.

My 2013 Hybrid build date Feb 2013 works with 3.10. I installed it myself. (takes a while to install). Difference might be I installed starting from 3.8 not 3.6. I think the main changes from 3.6 on were for phone updates. Read the release notes from each release and see if you think you would benefit with upgrading.

Originally Ford said the approved way of updating to 3.10 was via dealer using IDS, they weren't going to push it out through the owner.ford.com website. I have also updated via an image on USB, I had to search for a copy with google. 3.8 (or 3.08?) seems to be a worthwhile upgrade but I'm not sure 3.10 is that worthwhile - as other have said it may have introduced a few bugs as well. When I ask voice to "Play Track 1" it wants to know if I mean track 1 on the CD or track 1 in my media library and when I say "CD" it says, "That's not a valid track number for this disc" - then it says "CD" and I say "Play Track 1" and it goes ahead and plays the first track on the CD.

I cannot tell for sure what the dealer's tech did but I assume he went straight to try installing 3.10 The problem is that I cannot seem to be able to download the file I need for the USB stick to do it myself. When I go to https://owner.ford.com/tools/account/how-tos/keep-your-sync-up-to-date.html the website shows " You're all up to date. Your vehicle has the most up-to-date SYNC software." with no file to download. But it the car, it shows 3.6.2 ( SYNCGen2_4.30.13171_PRODUCT )... Supposedly the dealer (Ford Store Morgan Hill) has opened a ticket and will contact me when they get resolution...

I did this update last week via USB stick. Installed without problems. You have to leave the car turned on while updating. My gas engine just turned on for a few seconds during the update, I think it took like 20 minutes or so. The update will store an xml file on your USB stick that you're supposed to send to Ford so that they 'll know you've got it. I didn't see much difference yet, except one thing....before the update, I was not able to enter my password for my home wireless network completely, after the update it worked like a charm.