4.0 spark on 1,2,3 No spark on 4,5,6 I am losing my mind.

This is a weird deal. I can't offer any help but I hope you get it figured out. How about laying out exactly what you've done in chronological order?
Like:
swapped motor
then swapped ECU
then reset immobilizer
etc.
So it's all layed out in order so hopefully someone smarter than me can look @ it & go BAM! You forgot xxxxxx.

 

Do you have a way to check if you have any codes, such as an Ultragauge or Scangauge?

Let's make absolutely clear about cylinders.

1,3,5 are all passenger bank. 1 closes to the radiator.

2,4,6 are driver side. 2 closest to the radiator.

That being stated, your stated lack of spark matches the firing order that I just laid out?

 

I have some new info. The camshaft sensors from the blown engine had 2 wires. The good engine had 3. I switched sensors to have them plug in from the wire harness side. I did not pay any more attention to it than that. Today I took off the valve covers to look if the timing chain had been stretched. I noticed that it had, but that was not all. The vvt-I sprocket contact's were completely different. I thought all 4.0's were the same. So this may be the reason sometimes there was spark and sometimes there was none. I am doing a timing chain while I am in there, so I have to wait for parts. I will get some photo's when I get a new memory card. This has to be the reason. All the rest of it all works.

 

The first comment about cam sensors, and I did not have to read any more.

You have an '03-'04 4Runner engine, in there now. You have to swap the intake cam gears from your blown engine, into the one in your truck.

 

Then the spark will be back right? I love learning the hard way.

 

Its a common mistake and easy to do. When i have a junkyard engine dropped off to go in a car, the wrecking yard will often chop the harness off right at the connectors. I always check them really close and compare pin count, connector style, etc.

 

Mind Found!!!! So It is ALIVE!!! As it turned out, it was the vvti cam sprockets. I Had one photo from the good engine with the valve cover off. It looked like the timing chain was loose. I took the valve covers off to check timing. This is when I finally saw the difference. The sad thing is I changed the sensor from engine to engine as one was a 2 wire and the other being 3. I never thought to question that interior components could be different. Here they are. 1st is the 04 and the 2nd is the 06. No wonder the spark was not hitting on time.

 

Bravo. Glad you were able to overcome that.

Easy fix.

Did you purchase the truck used? Those cam gears have really broken down sludged oil caked and burnt onto them.

Whatever the case, some fresh lube at a shorter interval will keep your new-ish engine running a long long time.

 

Both engines had 200k+ miles. I got a steel on the 4x4 with a blown engine this Feb. I had the engine in the garage since December of 2017. This whole time I wondered what I was going to do with it, LOL. This is what it looked like when I brought it home, knowing nothing of the engine if it ran or how many miles.

I did get a look at what it came from. It was a rolled 4runner. I had been picking parts off of it for years