No problem.
Since my site it back up (knock on wood) you can see what I have/what has been donated at this url:
http://www.purrsiathunder.org/epscripts.php
Basically, the season one stuff must have been un-finalized versions of scripts for there are certain pages where the dialogue is different than the aired finished product. The ending of Sixth Sense in particular is interesting - in the draft I have posted, that famous Lion-O/Cheetara pairing hint is left out only to be added, obviously, at some later point. So what does that mean about the date on the cover? I’ll have to ask around…and try to get ahold of production crew that might actually remember what they mean. I talk mostly to writers and voice actors, and a lot of times, they understandably aren’t sure about that end of things or just have a fuzzy memory about them after a few decades. I’ll see what I can do.
The season two actual scripts I have (not copies) are labled “studio”, and apprently, were used in the studio and are more final, if you will. Those have less discrepencies, and others I’ve seen do have last-minute changes and notes scribbled in them. I’ll have to see if my first season script guy has a second season script (he does have a few) that’ll match one of those studio ones out there and see if the dates differ. That could tell us a lot.
There are other episode listings on the site, where one can compare and contrast how the lists differ. On my board, I had made a post that compared part of season one between the various lists:
http://www.purrsiathunder.org/tebforum/index.php?topic=181.msg2259#msg2259
One is the old, “traditional” listing, the “air date” list WB followed on the dvd, and the production or script # list. I too had thought WB would pick production over the air date list, following the MOTU mold.
I will say the air date list gleaned off the pazsaz site is screwy, given the dates we can clearly see on the late series scripts. No way they could have aired beforehand (in 86, which most season two eps have on the air date list there - nevermind the scripts I have say 88).
The “modern” list was what was on most web sites when I came on the scene in 2001, and everyone was just copying everyone else’s ep order. Where it originated from I’ve no idea, although I did notice CN tended to air reruns in that pattern. Perhaps it’s just an idealized ordering, in a way that made more “sense” to fans (i.e. keeping the trials together and so on). I would think maybe the list originated at the Ultimate site…because it is the most ripped-off site by others of all time
You see that site’s info reposted everywhere, for better or worse, as the case may be.
If you follow the Cover links on the script page of my site, you’ll see the ep #'s and dates listed on the scripts available. Finances/donors willing, I may have more in the future to offer.
As was said, the season one order has been confirmed by the fellow selling copies, and I have confidence that season two, as with most lists of eps, follows the proper order too. It’s rarely in any other order no matter what list you look at, and is the least disputed as far as sequence - how to split it up (as to whether it should be divided into three more seasons or kept together as “season two”) is another matter. WB, obviously, considers it all a whole season.
To get to your questions, I was under the impression that these were production numbers, but I can always ask around and double check. I’m also pretty sure people like Peter Lawrence and other writers have confirmed in the past that the eps were often created in an order contrary to how they aired and so on. Much like, it sounds, MOTU was.
Personal opinion here, I do prefer the Anointment Trials together as the story does imply those took place one after another (consecutive days in the cartoon’s universe) so it makes more sense to see them together. But then, it doesn’t bother me to see them split up on lists and on the DVD either. The sun still rises and sets either way 
Phew, shutting up now. If I learn anything more that is helpful, I’ll let you know.