"I was wondering if anyone can tell me all the differences between the NF and NG code engines. Is the only thing different the intake manifold and where the injectors go? Speaking of injectors, will my 4000 cis-e injectors plug in to the head/ manifold? Lastly, do both engines have the same cam, and the 40mm valves?"
See below, yes, yes, and yes.
I'll list the differences one more time. Please listen louder...
The NF and NG are identical from the oil pan gasket to the head gasket.
Generally, the NF is used in the "big" cars (5000/100) and the NG in the "little" ones (cgt/80/90), although some 100's have the NG style head - on an engine called "NF." No one knows why.
The big car oil pan is a bit different - there is a "dent" in the little car oil pan to allow room for the radiator and AC condenser. (All 10 valve I5 oil pans are interchangeable except for this little difference.)
From the head gasket up there are radical differences. The NF looks like your 4000/Coupe engine, except for the lack of a vacuum pump. The intake manifold is a bit different but bolts up exactly the same. This is the engine you want to use. You use your fuel and exhaust system, and it is plug and play.
The NG uses a two piece intake manifold, and the injectors are mounted in the manifold. If you want to use this engine you will also need the fuel injector lines as they are routed differently, and the black boot from airbox to throttle body, and all the clutter on top of the intake manifold (cruise, throttle stuff, etc) since it is different. Your throttle cable may not be a simple hook up either. These heads also have the vacuum pump for brake assist (in addition to engine vacuum).
You will use your engine mount brackets. You will also use your old distributor and cam cover, in order to use your engine management system intact.
There are many pictures of an NF being rebuilt and installed in a 4000 Quattro, this file is the first of a series of about nine!
"Which is better to swap into a 4000 Quattro? I am going to use my fuel and ignition system and my intake/exhaust manifolds."
The NF, hands down.
"Do these engines have more low end torque than my 2.2 JT? Lastly, should I use the whole long block, or just the short block with my head and my 38mm valves?"
Yes they do, in fact, they have more over the entire rpm range. Use the whole long block.
"So the NF engine is the one I want. I think I remember that it became available in 5000's in 1986. How can I tell that I'm getting an NF instead of some crappy 2.2 that someone swapped in when they broke their NF, is there a code on the block, if so how do I decode it?"
The only things I can think of are the knock sensor bolted to the left side of the block and the transistor booster thing that fires the coil. Oh yeah, and no vacuum advance servo on the distributor. But to tell if it was retrofitted with a 2.2? No real way to tell if someone actually did something as foolish as you describe. The way I would tell under such circumstances (unknown or unsure used engine) is to check for the little oil squirter nozzles in the block under each piston. To do this the oil pan must be removed.