2000 Ultra starts but won't stay running
 

Ok here's my problem. Turn the ignition on bike cranks fires up and runs for about 30 to 45 seconds and shuts off. I turn the ignition off for about a minute or so turn the ignition back on bike fires up and runs 30-45 seconds shuts down. You can hear the fuel pump relay click when it shuts down and click when it resets. I have replaced the relay no change. The run/shut down time is consistent and does not change. Here's what I have replaced so far. New coil,new fuel pump,new 50 amp main breaker,new voltage reg,new crankshaft position sensor,new battery,new ECM. What ever is causing this is shutting off the fuel system but I am as far as I know what else to change or look for. Has anyone run into this problem or have any ideas what to look for? It is not throwing any codes either. OK just to follow up I have found my problem. It was a bad bank angle sensor. I replaced it and the bike is running as it should.

Have you unplugged the fuel line at the tank and reattached it? Lots of folks have problems with the check valve sticking.
As I understand the fuel system on newer bikes when you turn on the ignition the ecm powers up the system relay which powers the fuel pump. If the ecm does not see an input from the CKP it shuts the fuel pump down after 2 seconds. Hit the starter CKP sends output to ecm and the fuel pump comes alive again. sounds like you replaced everything.

Hey Vernal thanks for the reply. That was one of the first things I tried.