This could have more reasons than the above mentioned problems/solutions. ESP. when using a motogadget.
Which wiring diagram was the foundation for your m-unit?
Do the following wires share the same relay(s) or the same powersource: ecu, ignitioncoil wires, fan, fuelpump or a combination of these
the several other possible options to the above are:
option 1, you either have separated power cables running from the battery 1 for the m unit with fuse and and other(s) to relays.
If this is the case its most likely overdrawing your battery when your fan starts, or even worse when your fan is locked up. then it draws way to much voltage and your bike will shut down.
This can also happen with other relay connected components. (sounds most logic when it happens after about a hour and starting afterwards)
option 2, no fuse (40 amp) and are overdrawing the battery to run insufficient voltage to the ecu.
This can also happen with Insufficient resistance (thickness) for the powercable. For example Noco powersport batteries or other lifePo4 batteries have overdraw protection which will result in exactly your symptoms.
Option 3 A wiring issue (most likely the alternator blue wire) <- if this were the case you'd have to charge your battery btw.
this needs to be connected to a 12volt (or less with resistors) outlet to charge your battery properly. Your m-unit would still give out power to the attached leds cause they draw very low voltage.
Option 4 Your grounding cables might have an issue or insufficient grounding or thickness for whatever happens after a hour, with yet again the possibillity of your fan starting.
Therse a pretty easy way to test overdrawing and insufficient anything, just have a spare fuse ready because you may blow your fuse when its wiring or drawing power related.
Set your bike in neutral. Set your blinkers to position lights at a higher percentage open the throttle and start your bike with throttle opened, not fully, 1/3 half maybe.
If your leds start to flash or when you blow the fuse you have to change the wiring routing.
After this you could additionally test it with your bike in neutral and fully opening the throttle with a quick wrist flick, if lights starts flashing it probably of the 4 options with 3 being the least likely.