Sounds like you've still got a lot of air in the system. When you get that far into the fuel system, it can take a lot of pumping with the primer pump to purge the system. Did you fill the new spin on filter with fuel before you put it on? If not it will take a lot more pumping to purge the air. You should have a bubble in the primary fuel filter, but it should be a small portion of the filter. If it's mostly air you've still got a air leak. Make sure all your hose clamps are tight. Also look for air in the hard plastic return line from the injection pump to the fuel filter, if you can see through it, is there bubbles. If so more purging is needed or you've got an air leak.
You might also try cracking open each injector line at the injectors to purge any air out of those.

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