I helped my son install an 89 302 in his 88 F150. Its been a nightmare trying to get it to run right. The replacement engine was complete, including the under hood wiring harness. All of this was installed. The truck wouldn't start from the get go. I diagnosed a bad ground to the distributor. I ran a new ground wire, and was able to get truck to run.
However, my son had issues with the truck with the old motor. He had replaced several items, and he put them on this new engine.
Map sensor
IAC
TPS
o2 sensor
Fuel pressure regulator.
Yesterday we could get it to run, it idles quite well. However, if you open the throttle, it will start knocking a couple times then die. If you open throttle slowly, it will accelerate. We checked fuel pressure, it was 40 at idle, but would drop as you open throttle. He has 2 tanks, and he's replaced the pump in the front tank . We ran out and got a high pressure pump for the frame and installed it. Now the truck has about 35psi and it actually increases to 40 when you open the throttle.
We checked for vacuum leaks, we sprayed all around with carb cleaner. We had plugged vacuum to brake booster, we know its bad.
We still have the problem with a knock then engine dies when throttle opens.
Timing is correct. OK lets hear some ideas

 

First mistake was using the donor engine's wiring. Always use your original harness, that way you know everything is the same.

Step 1 now would be to pull the codes and see where you're at.

 

Did you remove the spout connector when you set or checked the timing? Or was the distributor never removed? Just a thought.

 

Actually we did use the original harness. We had it running on it, but changed it with all the issues we came across, one of which was an intermittent non run issue. So the issue stayed with both harnesses. I found the bad ground to distributor after changing harnness. The real issue now, why does it ping then die when you open up the throttle?

 

Pull the codes.