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There are only 3 things that I can think of that would cause the motor to backfire out the intake on cranking.
1. The ignition timing is off and spark is occurring when the intake valve is still open, or
2. The valve timing is off, either was set up wrong, or the chain has stretched and slipped a tooth or two on the cam gear causing the intake valve to still be open when the correct ignition timing fires.
3. A stuck open or bent intake valve on a motor that is pretty worn out or was abused.

If the motor was running good before you did your distributor swaps then of course you would suspect the ignition timing.
Double check the rotor under the cap and all of the routing of your plug wires.
You can also check to find TDC of #1 Cyl by removing #1 plug and using a compression gauge. This should verify that you have compression near where your timing mark on the crank is telling you that you are just before TDC of #1.

Here is the 4.0L Firing Order again:
 

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Sometimes you can look at something several times and not notice that something is wrong. It would be a good idea to have a friend double check the position of your Distributor at TDC #1 and also the routing of each plug wire from where it is suppose to be in the distributor cap to the correct plug and cylinder.
It's easy to overlook something or think that it is correct when it's just one click off. :)
 
Ok, so yet again I’m here posting a failure. I found TDC using the chopstick test, The dizzy is on number one, everything is set “correctly”. But when I found TDC I noticed that the tick mark on the harmonic balancer is no-where near the 0 on the timing pad thing attached to the block…. It’s about 2 or 3 inches past? I have a massive gut feeling that, that means something wrong… I’m going to recheck the firing order again. But, here is the strange thing. It fires through the intake for one pop and then turns over normal… It’s like every time I turn it over the first time it pops through the intake? It never does it again for as long as I’m actively cranking it over… Any input/ideas??? I’m almost thinking cam timing sadly…. Please tell me it isn’t so!
Let's start over.
Crank the motor over, by hand with a breaker bar on the harmonic balancer nut if you have to, until the pointer on the block points to about 10 deg before TDC on the timing strip on your harmonic balancer.
Check the position of the rotor in your distributor, it should just be about to point directly at the #1 plug wire contact in the cap. If it is not pointing more at the #1 than anywhere else then you have your distributor in wrong.
I'm "old school" so I'm a little disadvantaged here, but the last time I replaced a distributor, it would start into the hole, make contact with it's drive gear on the cam shaft and would turn slightly as you pushed it down into where it needed to be. So you would have to anticipate just how much it would turn at the end and allow for this when you started it into the mounting hole. Always double checking that when it was seated that the rotor was pointing at the #1 plug wire contact in the distributor cap.

Now you said that it would fire back up the intake and then turn over normal.
If you can turn it over normal without a lot of intake firing then you should be able to hook up a timing light and use it to verify that you indeed have the timing set correctly.

If you do all this and verify with a timing light that the timing is set correctly and you still have this problem, THEN it is time to suspect other things such as the valve timing or a stuck open intake valve.

I hope this helps, I am not very familiar with the new electronic ignition systems so I may have overlooked something here and I hope someone younger and smarter than me can jump in here and help.

Woody
 
I would go buy or borrow another timing light and a compression gauge.
The compression gauge will help determine if the valve timing is correct and which cylinder has the problem.
If the basic mechanical stuff is correct then there are sensors such as the crank position sensor that could come into play.
I'm not too savey on the sensor stuff so hopefully someone else will jump in at that point.
 
If you are turning over the motor the same direction that it runs, then the exhaust stroke will always proceed the intake stroke and the camshaft actually keeps the exhaust valves open past the point of opening the intake valves so that the escaping exhaust gases will help draw in the intake fuel charge (overlap).

I see from an earlier post that you replaced a broken Crank Position Sensor. Re-check the CPS. Also recheck the fuel pressure at the fuel rail. If it has fuel and spark and the timing is correct, it should at least start even if it runs rough.
What other sensors did you change that could cause a non start and why did you change them?
So many things have been changed or modified on this swap that it is hard to pinpoint just what is causing your problem.
You say that this new '98 motor was running good before the swap, so maybe you need to backtrack to take another look at all that you changed.
Is it really that difficult to wire in the '98 Distributor that came with the motor instead of using the '97, as you said, I don't know why that would make a difference but at this point you try to go back to what was working.
 
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