Concern After Removing Front E-Shaft Nut
 

I might be reading waaay too much into this, but here goes:
I am changing the front cover on a S5 engine and obviously I needed to remove the front bolt. I've read all the horror stories about the torrington bearings getting crushed and so I read over Mazdatrix's writeup several times. I saw any work with the engine out of the car (which mine is) needs to be done with the pulleys facing up, flywheel facing down. So I rotated the engine on the stand with the pulleys up, flywheel down, and had someone hold onto the flywheel with a flywheel tool while I loosened the front bolt. He said that as soon as I loosened the nut, the flywheel dropped a bit. Now I'm concerned that I did something wrong or missed a step, as I'm pretty sure having the rotating assembly shift is exactly what I needed to AVOID. Could someone clue me in as to whether this is normal when pulling the front bolt, and if not, how and where do I check to see if my bearings are still in place?

The front bolt holds tension on the whole front stack, this isn't uncommon when you break the front hub free. After its put back together and torqued down is when you want to make sure its thrust play is in spec before running the engine.

Okay, glad to hear it's not uncommon. Is there a way to check and make sure the bearings didn't shift when the rotating assembly dropped BEFORE torquing the front bolt, though? I've read that torquing it with the bearings out of alignment is exactly what crushes them.

If you are changing the front cover you will be able to check the spacer when the cover is off to ensure it is inside the Torrington bearing and not on top. You will see what it does after you have it apart. You will also see why the e-shaft dropped, because the spacer and bearing support the e-shaft and keep it centered.

If you have the front cover off already you can pull the stuff off the front stack to verify the torrington bearing is still in place(the spacer hasnt moved). Given the engine was sitting on the flywheel when you busted the nut loose it SHOULD still be in alignment.

Aha, see, everything I had read said "pulleys up, flywheel down" so that's how I set it up on the engine stand. I didn't set the engine on its flywheel. Thus, when I popped the bolt the whole rotating assembly visibly shifted downward, and that was what concerned me.
Luckily I was able to pull the counterweight up some and see that the front torrington bearing was still BARELY on the spacer, so I had some friends lift up from the flywheel and wedged it with a jackstand and board. Oil pump gears are in perfect alignment now, so I'll take that as proof that everything is in alignment now.
Amazing how I poured over all this info for months and still didn't catch that people set the engine on the ground.