Unfortunately this has not changed the situation at all, I can still upload but the sketch will not run.
I have spotted something I can't explain, perhaps someone can. When the sketch should be running, and during sketch upload, GPIO0 measures around 1.7V~2.1V on my DMM. GPIO2 is rock steady at 3.3V. If I hold down my reset button, GPIO0 also measures 3.3V. The last sketch I had running used GPIO0 as the SDA line of the i2c bus. Could this be a clue?
I am going to order a replacement esp-01 and an esp-12 to continue my project.