I had the same problem. Your computer still thinks your running a 2.5L with injection so its priming the fuel system. That's where your 3 seconds is coming from. But the computer is no longer getting a signal from the engine that tells it that its running so it never energizes the fuel pump relay. That's where your problem is. It's a very simple fix and there are 2 ways to do it. First would be to run a new wire that's hot while the ignition is on to the fuel pump. Or you can do what I did and remove the fuel pump relay and run a jumper wire using to crimp connectors and a really short piece of wire.
Here is a pic of what mine looks like.
