water flow seems fine all though a little low.
confirm that fault is common to central heating and hot water.
if 1.5 years old unlikely to be mechanical fault.
at a guess gas valve, avp or pcb
this mod would explain why universal thermocouple works and pilot is cutting out due to overheating.
the apollo relies on a minimum rate of flow of water through the heat exchanger(i believe it is stated in the manual).
well spotted tony
i would advise you to put the old thermocouple back because it has an interrupter in it you can not use a universal thermocouple.
the common problem with these boilers is circulation i would recommend that you replace the pump