I replaced the old thermocouple with the one from my multimeter. I decided to let it hang louse so I can place it against the pcb during reflowing..
I have the PID loop working. After I programmed a reflow cycle it became obvious that the electronics compartment got to hot. So I replaced the fan by 2 50mm fans.
The problem is that these draw much more current then the old fan. Therefore I had to add a second power supply. The fans can still be switched by the main print. I chose a switching power supply so that I didn’t generate to much extra heat in the electronics compartment.