Hello Bengt:

What type of fuel pump do you have - Round Hausel or small brown colored Flight Works ? I just would like to know.

IF the fuel pump was run dry at any time during operation, it could have been damaged. It is possible that what is happening is that the pump is trying to get the engine up to speed but will not do so as it may be hanging up and then releases then hangs again. The fact that your problems all started with the discovery of the air leak in the fuel fileter which is located on the INLET to the pump may have had an impact on the pump.

Remove all fuel delivery lines to the engine and solenoids and blow out, including all fittings to insure that there is not dirt in any of them.

Disconnect the pump from the ECU and connect a 1.2 volt "D" cell flashlight battery across the pump and check to see if it has smooth, constent rpm operation. BE SURE to pump fuel thru the pump while performing this test.

Re-connect all tubing and restart the engine.

As for the thermocouple, they do not as a rule, pulse the engine as you have described. I belive that your issue is in the fuel delivery.