Assuming that the H & L limit screws are properly adjusted, ideally for each remaining sprocket is the upper pulley supposed to be perfectly aligned with it when shifting?

Yes, but the limit screws aren't what you'd adjust to set that alignment. You'll need to adjust the cable tension (indexing adjustment) to get it there.


Park Tool has a great guide for rear derailleur adjustment:
https://www.parktool.com/blog/repair-...nts-derailleur

I've never looked, I adjust the derailleur for smooth shifting and let the pulleys end up wherever works. Same with adjusting the limit screws, just loose enough to allow a crisp shift and no more. I doubt that a good job can be done by eye. Follow the Park instructions above and you should be fine.

The only sprocket for which the RD's position is determined by the limit screws is high (outermost). All other shifting and trim is set by the cable length adjuster. The low gear limit only prevents overshifting beyond the inner cassette sprocket.

I do it by ear. If it's off you can hear chain noise in some gears. Should be quiet through all the gears in big and little. I check when I'm done and it's centered when I do it that way.

Pulling the cable tight and then seeing if it will shift one gear with one click on the shifter, adjust cable until it goes into gear and then see if it will go through all gears without noise, adjusting as necessary. Takes a couple minutes after you've done it a dozen times or so.

^^ That's how I adjust my RD until it shifts fine through all gears. But the other day I was just looking at it from behind and noticed that when in one of the midle cog, the upper pulley is slight out of the plane down toward the smaller one. I decided to adjust the cable tension to move it up a notch into the same plane to see what happened. Well, the only thing that change was the shifting was just a tad slower going into the smallest cog.