As I read the original post describing the problem, I had just experienced this very same type of issue and thought I how ironic to see this.
I did all of the very same troubleshooting to search for my problem. Long story short, My motor was a Jet Munts 200 and my issues started in a very same manner. I had never had a flame out since owning the motor over several yrs of use. Mine flamed out about 5 minutes into my flights with no visual signs. I inspected fuel system and checked all my cables after first flame out, even tried a different battery. After second flame out on my next day out to the field, It turned out that I found a loose screw mounting the motor's front circuit board. Tightened the screw and checked all wire soldered points on board. I didn't change anything else. Took plane back out to the field this past Saturday and got my flawless running motor back again. 3 great flights.
I know this may sound strange to some, but this is my personal experience over the past couple weeks. May be worth looking at and good luck with your troubleshooting.