Done this swap many time but can't remember exact details, you need to set the auto transmission position sensor to park or neutral (dial lobe that sat on the auto transmission). If you unplugged the dial from the harness you have to jump two pins on the harness plug for that sensor, it acts like the clutch pedal safety neutral switch.
I have answered/given this info in proper full detail to someone on this forum, search auto to 5speed swap in 1G mx6 forum with replies posted by me. you should find all the details and steps to follow to get the car running.
Did you remove the auto box behind the steering shroud (the one holding the speaker)?
To test/run the fuel pump there is a yellow plug on the strut tower, it sits next to the green test connector, on left hand drives its on the drivers side strut tower. this yellow plug has two female spade connectors in it, you need to jump them (connect them together) with the key on and see if the fuel pump runs. But if you are getting 12v at the fuel pump harness plug than the pump is no good.
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