I just replaced the crank seals and the generator side of an AT3 is more difficult. I figured it all out to the point of reinstalling the armature and stator.
I can't seem to get the armature on far enough for the dynamo cover screws to reach the threads. I have tapped with a hammer once the armature is on and keyed, but when I place the cover over that and try to tap it far enough the catch the screws the whole thing, armature included falls off.....

Whats the trick? I don't want to beat on either to hard to break it....

Did you install the brushes I believe you install the brushes after the cover is installed I’m getting ready to start restoring an AT2 soon

Yes I forgot to mention that. I bought new brushes and made sure they are out of the way before trying to reinstall over armature… 
 

I'm not sure I completely understand but I think I do.

Taper on crankshaft and inside armature needs to be spotlessly clean and dry.  Install armature to crankshaft being extra careful to make sure keyway is aligned, install "governor" (points cam/advance piece) and tighten bolt.  This should lock armature to crankshaft if key is aligned and taper is in good shape.  Remove bolt and governor and install stator over armature. 

If armature does not lock to crank after bolt is tightened then there's an issue with the taper, key, or keyway.  You will have issues if you don't get taper locked. 

To expand on above...  taper is the primary "hold" the armature has on the crank.  Key is butter soft and while does provide a little force to keep armature from spinning on the crank, key is primarily an "assembly aid" to index the armature/governor in the correct position for points timing. 

Machine tapers are common and very strong connections...  most drills have the chuck locked to the spindle only by a taper.   Lathes and mills also use tapers to lock tools and and parts to spinning shafts.  No key required. 

 

OK, I have tried this 2 ways without success. If I slide armature into stater cover before i slide to crank the armature comes all the up to its perfect position in the cover... BUT when I try to install both at once the key gets pushed back and holds it all from sliding back into place. I cant get the cover to mount straight and I can't a line the screw to thread.

The other way is one at a time. Once I have the armature on then getting the cover on straight is almost impossible. I can not get the armature to slide up inside the cover all the way.... Something is holding it back and its NOT the new brushes. They are out of the way.

Im doing something wrong or missing a step....

I don't remember ever having that issue.  We can't see what you see.  Only other question I have is if the generator parts are original to bike and were previously assembled on running engine and removed by you? 

There was a change made in the later years...  earlier AT1 models had a slightly smaller armature.  Possibly mix and matched parts that don't belong together?  Maybe early armature in later stator?  Just wild guessing.

MarkT
I followed your directions and locked armature against taper. Then tried putting cap over armature and it does not slide down where armature center fills up space on cap center. Still brushes are out of the way.
The front part of armature that the brushes ride on just does not seem to want to enter that area of the cap... Seems to be hitting something but I cant see it.
If I drop the armature into the cap before installation it falls right into place...
The bike ran great before taking apart. All parts fit together before pulling to change seal.
 

Post some pictures sounds strange 

If everything you are trying to fit came off that crank then it must go back on. Sounds like the crank key is curling up out the back & stopping armature going all the way. If that's the case just tap it down flat in line with taper angle then eyeball the key slot in armature directly over the key. Has to work unless you've replaced the crank key with something that's too tall. Just be sure key is fully in groove & doesn't sit up very tall, in fact very little. Other important thing with the outer bit field coils-stator thingy 'is' it has small pins in that crankcase to locate it 'i think' but if your long screws are finding the threads in the case then you have to have it on the pins--i think. Been 50 years but my long term memory's ok--[what was the question lol].