Hi Rob Im Scott
I believe you have a problem somewhere in your fuel lines or your pump has a problem, if you trace all the lines from engine right back to the fuel tank and look for any sign of leaking fuel, also try making sure the tank is filled right up and see if it still happens (to rule out holes in the pickup tube inside the tank or the pickup tube having come off)
try running the fuel line like you did before from the filter all the way to the tank. This will effectively eliminated everything but the pump. check for bubbles in the inline filter if there are then you have air entry into the pump. you can also replace the fuel line from the filter to the pump with a clear pipe this will enable you to see any bubbles and if the lift pump is working correctly. Above all ensure your filter is clean failing these options working for you I would suggest that the main fuel pump itself is in need of overhaul, this is an expensive exercise. I have however heard that there is an option of replacing it with an electric pump which will ensure you dont have any more problems like this in the future and I have heard its much cheaper too. I cant give you any info on these as I have only heard it by hearsay but It may give you an option.
The clicking noise you can hear is the lift pump relay this could also be faulty they are a cheap replacement and i recommend replacing this as a possibility also.
I know the above seems long and drawn out Im sending you all the possible info i have to attempt to help you 1st go.