The MODX is connected to my laptop through USB.

I am trying to sync all machines to midi clock, but I can't get it to work.

Reason only sends clock out to 1 port.
The midi ports on the MODX don't work in a normal fashion in USB midi mode.

”...in a normal fashion...” ??? What is a normal fashion?

MIDI I/O = USB
When you are connecting your MODX to your computer via USB, you need to set the MIDI I/O = USB, when you do so, the MODX itself sends and receives data on USB Port 1. In this configuration the 5-Pin MIDI jacks work to connect an external hardware device to and from the computer, as Port 3. All data arriving at the 5-pin MIDI IN goes directly to the computer, all data routed from the computer on Port 3 arrives at the 5-pin MIDI OUT.
You’ll need the “Yamaha Steinberg USB ASIO Driver “ for your Mac or your Windows PC, when using USB.

MIDI I/O = MIDI
When you connect the MODX to an external MIDI interface using 5-pin cables, you need to set the MIDI I/O = MIDI and then you can turn the MIDI THRU = ON. This allows the incoming MIDI to travel through the MODX (effectively turning the MIDI OUT port into a MIDI THRU Jack.

You do not give several critical details here:
_ Tell us a general description of the “Elektron Model: samples” (?) (assume I work for Yamaha and perhaps don’t know what that is or how it connects to the rest of the world...? 5-pin MIDI, USB, other? Can it be a master clock? Can it be a slave to clock?
_ What version of Reason? You mention you are using it as your DAW (there are options to run a Reason as a plug-in... this maybe one option you’ll have to use - if as a DAW it can only send clock on one MIDI Port and you need to send on multiple Ports. (A DAW like Cubase can transmit clock to all connected devices and can run Reason as a plug-in).
_ I’m guessing your question is how to hook that Elektron device up to your computer or how to get clock to it - (?)
which type of computer, you also don’t mention, Mac or Win?
_ Do you have an external MIDI interface?

First things first:
I recommend you setup Reason and the MODX.
Get those two items working with each other. Get them to Sync. (With this we can help you).

If Reason only sends clock on Port 1, you’ll need to deliver Port 1 from Reason to all your devices that can follow clock.
When setting up with the MODX via USB send clock on Port 1.
When setting up with the MODX via standard 5-pin MIDI, send clock to the device acting as the MIDI interface.

When the MODX is connected to your computer via USB-MIDI, using the proper driver, the computer will see the MODX as a device with 3 MIDI Ports:
Port 1 — addresses the MODX tone engine, for music data, controllers, and clock
Port 2 — reserved for future functions
Port 3 — addresses the 5-pin MIDI jacks on the MODX back panel.

If you connect the MODX via 5-pin MIDI cables, Data arriving at the 5-pin MIDI jack can be routed “Thru” by connecting the 5-pin MIDI Out jack to the next device... and setting MIDI I/O = MIDI and setting MIDI THRU = ON

Extra Credit:
The MODX can generate MIDI Clock and it can receive (slave to) MIDI Clock. Most Audio devices ‘like’ to be Clock source (master clock). It takes significant processing muscle to adjust audio to an external clock; and in comparison, it takes less processing power to slave MIDI to audio. There is also a limit to how far you can time stretch audio before artifacts are noticed (mileage can vary), versus adjusting MIDI which has zero negatives sonically. This is something to consider if you plan on using audio samples and MIDI, sync’d.

Thanks Bad Mister for the response so far 🙂

I'll update the critical details first.

I run version 10.4 of Reason on an ASUS I7 8GB Windows 10 laptop. So I cannot run Reason as a VST inside another DAW

The Elektron Model:samples is one of Elektron's sampler/drummachine/sequencer grooveboxes. It can connect through both USB and Midi simultaneously. It has a midi in and a switchable midi out/thru. Both of them connect through trs-midi adapter cables. It is able to both be master and slave to midi clock.

Reason and MODX work together. I can sync the MODX over USB to Reason and vice versa.
I can also sync Reason and the Model Samples both ways.
I can even go DAW-less and hook up the MODX and Model:samples over 5pin midi and sync them both ways.

My question is indeed how to get all the machines hooked up so that they will respond to start/stop messages and sync to midi clock.

RIght now I have the MODX hooked up to the laptop over USB. It also acts as my soundcard in Reason (ASIO Driver) and as my "master keyboard" to play MIDI into Reason.
Reason can only send clock out one port. So when I choose the model:samples, it will react to start stop/clock. If I choose MODX port 1 the MODX will react to start stop.
I just remembered that If need be, I also have a focusrite Saffire 6 USB audio card with midi in/out lying around.

I hope this is all the info you need to set me on the right (midi) track

The Elektron Model:samples is one of Elektron's sampler/drummachine/sequencer grooveboxes. It can connect through both USB and Midi simultaneously. It has a midi in and a switchable midi out/thru.

Okay both units can connect through USB and MIDI simultaneously, both units have a switchable MIDI OUT/THRU. Excellent.
On the MODX when connecting to the computer via USB the standard 5-pin ports act as a MIDI interface for an external device. — you can send clock to the 5-pin MIDI OUT by connecting your DAW to MODX (Port3).

Reason and MODX work together. I can sync the MODX over USB to Reason and vice versa.

Excellent.

I can also sync Reason and the Model Samples both ways

Excellent.

Things to try... What a major limitation that clock is only delivered to one port (?) at a time, I presume (?). Is there a reason? (bad pun)
Is it one port at a time or strictly only Port #1?
Connect the devices so that you can use can the THRU function.
Example, connect the sampler to the computer and THRU the clock to MODX. Standard MIDI 5-pin is always Port 1, so the 5-pin THRU jack should always be Port 1

Sorry, but you’ll have to experiment, I have none of what you are attempting to connect except the MODX.
Here are the known parameters about your Yamaha MODX
If you connect the MODX to the computer via USB for MIDI you must set MIDI I/O = USB
If you connect the MODX from a MIDI interface via a 5-pin cable you must set the MIDI I/O = MIDI
Standard 5-pin MIDI is always considered Port 1, and signal arriving at the 5-pin MIDI IN, is thru’d (duplicated) at the MIDI OUT jack when you switch it to the THRU function. Since both devices have switchable OUT/THRU and since Clock is sent to that THRU port... you can daisy chain the clock to the next device.

You’ve got time, experiment.

If you can only select the different USB Port devices individually, then you can workaround the entire limitation by connecting one device and render its MIDI data as Audio, while you work with and add the second device.