...essentially, Crowley found a connection within Hebrew stuff that supported original TdM stuff that was around before the Golden Dawn, and for some reason the GD changed it in the middle there somewhere which had its effect on Waite and his deck.
Not exactly. The Golden Dawn changed the ordering to better reflect the order of the zodiac so that you would have first the planets based on their speed of movement and distance from the sun:
Fool: Air
Magician: Mercury (closest planet to the Sun)
Priestess: Moon (next "planet" as far as the classical astrologers were concerned)
Empress: Venus (next planet out)
Now begin the zodaical Trumps beginning with:
Emperor:Aries
Hierophant:Taurus
Lovers: Gemini
Chariot: Cancer
Strength: Leo
Hermit: Virgo
Justice: Libra
etc.
These attributions make sense, since they follow natural progression. What Crowley did may seem, on the surface, as going back to the original order but what he did was so drastic and "out there" it can't be considered as such. Here, in order to understand that you really have to know your stuff, because it really is confusing. Here is a short, graphic explanation that serves mainly to demonstrate what niether I, nor you, will ever fully understand
http://www.cornelius93.com/EpistleonZodiacBelt.html
It has to do with the reception of the Book of Law and certain instructions contained therein. For the Thoth it works... after a fashion, although some would say it causes more problems than it solves.
Was/Is there correlation between Alpha and Omega for #11 Justice in the TdM, similar to Crowley's? Because LRichard has already shown me the Magician and Strength with their leminscate hats... which is similar to Waite's depiction of those cards.
I suppose esoteric significance can be found, but they aren't intrinsic. Many aspects of the TdM were discarded by both the GD and Crowley, and symbols were used differently. As for the TdM having no esoteric significance, that's simply not true. Even if we disregard everything else, the Trumps clearly show some kind of at least astrological ordering that was put in place originally, even if the deck was not finalized until long after its origins. Cards like Justice with its scales or Strength with its lion or the Empress with its Venusian figure all point to some astrological connection. But it would have been natural for the creators of the deck to include these figures at the time.