Does that little spring inside the boot have to be pulled up or does it have to be flattened underneath the rubber lining???

That little spring should contact the top of the plug. Mark the boot skirt position on the plug. Then Measure the depth to the spring inside the boot with a toothpick, and compare the measurement with the plug dimension above the mark you made.
Using a plug with a longer outside isolator may have overcompressed it, but probably there is nothing to worry about. The engine will function if the spring is too short, though you may generate some extra radio interference due to the spark jumping the gap inside the boot.

I've never taken off a DA cap, but the caps on my 3W's are really diffucult to remove.

3W has the little ring on the end of the cap that holds it together kind of.

Everytime I remove the cap, it feels like something is going to come apart...

If you follow the manual and use a small screwdriver to carefully pry evenly around the perimeter the caps will come off very easily with no distortion or the feeling you describe. Its a bit of a trick, but once you got the method down you know it as the cap comes off very easily. Its a good thing they fit very tight trust me!

DP

Cool! Are you referring to a DA manual?