I have seen that the CRS317 supports jumbo frames but when I boot SWOS I don't see any way to configure/enable/set the MTU. How do I do that?

I have the CRS305 and see in the docs that Jumbo Frames are supported but when I ping testing the JF, I get hangs and errors. The most I can ping is 1472 MTU.
Is this a setting somewhere. I am using SWos

One thing is hardware support for jumbo frames when switching between ports. And that one is not configurable, it's simply enabled and at switch-chip maximum, meaning that whatever frame size (up to HW limit) received on one port will be transmitted on another port as well. So devices, connected to the switch, should be able to use jumbo frames when communicating between them.

Completely different thing is support for jumbo frames for management connection (via web browser). I'm not sure if jumbo frames are supported in this aspect and it's best to use workstation configured for use of standard frame sizes when performing management of SwOS.

I recently set up a CRS309-1G-8S+ with two S+RJ10
Five machines are connected: three using Intel X520 based cards and two with Asus XGC-100C via the S+RJ10
I have previously had the two ASUS connected directly together and had set MTU as 16000 following comments in the linux "atlantic" module source.
The other three intel NIC machines had MTU set to 9710, again following a comment in the linux module source
All was well on any transfer involving an Intel NIC but on the Asus to Asus connection, the communication would just stop.
The CRS309's SwOS web page showed nothing wrong.
So no errors visible, but no comms.
After some head scratching I set MTU on the Asus NICs to 9710 and all worked perfectly.
It seems SwOS is taking no part in the MTU negotiation, even though the S+RJ10 is imposing a limit on MTU.
This is not a bug but it might be worth pointing out in the SwOS manual....

I have had issues where the switch would freeze and I would have to power cycle because some ports were using different MTU's. I find it is best to keep all ports using the same MTU, then there is never an issue. I don't think SwOS can do MTU fragmentation. Unfortunately there is always some device that only uses 1492/1500 so it is hard to go above that without issues. What I would like to find out is how to use, lets say 9000 MTU, and have all the other devices like WiFi router, printer, etc. that cannot be changed to work on the same local network. Is there a way to run a separate unmanaged switch for these devices? Or is our only option separate vlan's on a layer 3 switch?

There is no such thing as MTU negotiation. You're probably thinking about PMTUD which is IP layer function ... that's L3 while switches are L2 devices. Only routers contribute in PMTUD.
HW can have MTU limits (switches included) and when deciding upon MTU value to be used inside an IP subnet one has to consider smallest of HW limits (in case of switches equiped with SFPs either one can have lower HW limit). Inside L2 network PMTUD doesn't happen ... because packets arrive directly at final recipient and that box can either receive packet or not (in the later case incompletely received frame is discarded without any further action). The same is true if frame size exceeds capability of any L2 device on the path.
Only routers with interfaces set to different MTUs can receive large frames (when large MTU is set on ingress interface) and react (by sending appropriate ICMP message to original sender) if frame has to be discarded because it's too large for egress interface's MTU.

The ONLY thing needed here is a statement from Mikrotik regarding the maximum MTU physically supported by the switch-chip hardware in various devices.

The ONLY thing needed here is a statement from Mikrotik regarding the maximum MTU physically supported by the switch-chip hardware in various devices.

You mean like this? MTU in RouterOS

You mean link this? MTU in RouterOS

Yes, exactly like that.
The only odd thing here is that it is buried inside the RouterOS documentation, but is not referenced from the SwitchOS docs, and neither from the specs of the individual products.

All I know is the MTU issue was bad enough where I changed to an FS Switch and dumped the Mikrotik. No more issues with MTU.