1995 2.5L duratec intermittent start

1995 Mercury 2.5L duratec, auto, 86000 miles. Car quit running and I found that the front of car thorttle rod on the intake was gone, have no idea how long. They don't make the rod anymore so I made one, seems to work great. In repairing this I had to remove the phellum and found extreme carbon built up in the intake manifold. Removed intake and cleaned, replaced caskets for intake and phellum, replaced plug wires, plugs, gapped to.54 per manual, checked spark and getting a yellow to blue spark, but on DSI system I understand that this is OK. Had pressure regulator value checked at dealership and told that it is good, holds 25psi. Fuel pressure is 40 PSI. Had Coil Pack tested and told that it is also good, also changed PCV valve. After doing all this work I finally got the car started, had to pull the plugs once and clean due to fouling, from cleaning intake. Let warm up and took for a 18 mile test drive, ran the best that I can ever remember, plenty of power, blew out all the carb cleaner I had used etc. I also put some fuel injector cleaner in the gas, almost full tank. Got home, thinking it is fixed, turned off car, attempted restart and had some trouble but did restart, turned off tried again, no run. Tried and tried and gave up. Got up next day went out and fired right up. Shut off wouldn't restart, let sit 20 minutes, started right up, shut off, no restart, let sit 30 minutes started right up, shut off no run. I am confused, not real familar with fuel injection, just learning it, but I used to know the old cars real well. I'm 53years old. Justed started last couple of years to work on cars again. Current code is 543, fuel pump. I dont' believe it is the fuel pump. Turn key to on position and the pump comes on for about 2 sec, have 40psi of pressure, haven't changed fuel filter as I would think if clogged I wouldn't have 40 psi of pressure, nor would it run. I was told to try unplugging the MAF and try to start, but that didn't change anything. I think that all I've done. I am confused and lost, Please help.