Check that you got all the vac lines reconnected. MAP sensor on firewall to charge air pipe and tranducer down to EGR.
To prime the system you manually crank for 30 sec's at a time. Sometimes takes 5 or 10 times. Refilling both filters with fuel usually makes it quicker. When it coughs, it is usually necessary to keep cranking a few secs longer to make certain it is running. Doesn't harm anything.
If you see air in line #2, your leak has to be at one or the other end of line #1. If you changed the pre-filter, did you reinstall the big oring that seals it to the metal filter housing?
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Also check that all your fuel lines are routed properly.