Hi Tom,
I don’t think the files themselves will be the issue if you’ve used MakeMKV to produce them.
It looks like you have a network throughput problem. While your iperf3 test looks good in the reverse direction, it doesn’t look so good in the opposite direction. I would look at resolving that and suspect that once you do, your playback issues will disappear.
As you’re familiar with SSH, you could mitigate these issues (albeit this is not ideal) with autofs mounts. See File sharing with a NAS, media server, windows share or other device. If you are still able to log in to the box when you have issues, then this suggests that Kodi’s internal SMB connection has died. This can cause Kodi to freeze.
You can confirm if this is the case by seeing if systemctl restart mediacenter brings Kodi up again.
Sam