2005 Tacoma won't start

Hi, I have a 2005 Tacoma 4dr. v6 with the 6 speed manual transmission. let me give a little history on my truck, it ran perfectly fine until it sucked in water through the intake and hydrolocked. I pulled out the engine and installed a low mileage used engine. Now the truck will not start? it turns over perfectly fine. What I did notice is that the diagnostic light does not cycle when the key is first turned on? that leads me to believe the engine computer is not turning on. I did check all the grounds and did check that the computer is getting power at the proper pins. Has anyone ever run into this problem, I don't want to just jump to the conclusion that the computer is bad, could one of the engine sensors that went under water be shorting out causing it to back feed the computer? Ive had relays wired wrong do that before in custom efi builds. as of now the fuel pump does not turn on and the computer is not turning on the main efi relay as well as the check engine light (diagnostic light) does not cycle at key on. any ideas would be appreciated. Thanks