I think you should state what engine.  It's a 3.0 v6 right?  I don't know about the fuel filter being easy on those, it depends on where it is at.  Either way it will be a compression fitting filter, not an easy clamp on one like on the carbed trucks.  Also, the engine fuse will blow and the truck will still run?  That doesn't make any sense.

Definitly check your grounds, make sure all of them are there.  After an engine swap it is easy to forget one.  Also, the fuel pump is turned on by the air flow meter, then by the circuit opening relay.  If the air flow meter doesn't see any air it won't close contacts to turn on the pump.  This may let you start the truck, but then it will die, because its only running on the fuel it pumped when you first turned the key on.  Also, when you swapped out the engine, you had to disconnect alot of connections.  It may be that you have a loose, or dirty connection somewhere.