Ok, here's my take on it. I don't think it's entirely irreconcilable, but (Not to sound arogant or disrespectful) I disagree with JMS' episode order, which appears to be little-better than random, and ignored the uniform changes, and dubbing a couple extra lines of dialog.
My own order for the eps, based on internal clues and external logic placed 'em in this order:
0- "A Call To Arms" (The movie)
1- War Zone (Which barely fits continuity at all)
2- Appearances and other deceits (Where they get the bellboy uniforms)
3-Racing the night (Intended to be the 1st episode)
4-The Memory of War
5-The Needs of Earth
6-Visitors from Down the Street (The X-files parody)
7-Each Night I dream of home (The Lochley/Steven Franklin episode)
8-The Long Road (Galen vs. The Equalizer)
9-Patterns of the Soul
10-The Path of Sorrow (The Galen/Gideon/Matheson flashback episode)
11-Ruling from the Tomb (Lochley on mars/religious death cult episode)
12- The Well of Forever
13- The Rules of the Game (3rd Lochley episode, where the Excalibur docks at B5)
Episodes 2-7 are the "Bellboy" uniform episodes. Logically those would all have to be grouped together, since we see them *getting* the uniforms in 2, and Fiona Avery's "Bester" script had them getting rid of the damn things. Ergo, that one would take place between 7 and 8.
In going through these episodes, though, I've realized I miscalculated involving 2 of the Lochley episodes: I think I transposed 7 and 11, "Each night" and "Tomb." There's some badly-looped dialog in a scene where Gideon sees Lochley in sickbay and says "Good to see you again," which I've noted before, but discounted as an obvious add-on for the DVDs.. So I put that down as their first meeting as they're rather stiff, as though it were a first meeting. In "Tomb," Lochley recognizes Gideon, so I just assumed that came second.
In re-watching both episodes in close order, however, I realize this isn't the case at all: "Tomb" comes first. They're awkward in that, very professional, but clearly like each other, and just everything about it implies it's their first meeting. How did she recognize him? Well, duh, she's in charge of the conference so she'd have dossiers and presumably photos on every speaker attending. In "Dream of Home," upon re-watching it, I realize that, yeah, this was clearly their second meeting. They're more relaxed around each other. So I was flat out wrong about that. Also in "Tomb" Gideon says he's got 5 years to find the cure, and in "Home" he's already rounding that down to 4 years.
This introduces another problem however: those damn uniforms. Simply reversing those two episodes would mean they switched uniforms then back, then back again, then back one last time. The only way to account for all this in a way that would conserve the most amount of inter-episodic order, then, is this way:
0- "A Call To Arms" (The movie)
1- War Zone (Which barely fits continuity at all)
11-Ruling from the Tomb (Lochley on mars/religious death cult episode)
2- Appearances and other deceits (Where they get the bellboy uniforms)
3-Racing the night (Intended to be the 1st episode)
4-The Memory of War
5-The Needs of Earth
6-Visitors from Down the Street (The X-files parody)
7-Each Night I dream of home (The Lochley/Steven Franklin episode)
8-The Long Road (Galen vs. The Equalizer)
9-Patterns of the Soul
10-The Path of Sorrow (The Galen/Gideon/Matheson flashback episode)
12- The Well of Forever
13- The Rules of the Game (3rd Lochley episode, where the Excalibur docks at B5)
Which isn't so bad, really. It spaces out the Lochley episodes a bit better than they previously had been.
Just so no one has to dig out their disks to check, the DVD-order of the episodes is
1- War Zone
2-The Long Road
3-The Well of Forever
4-The Path of Sorrows (in which the crew make use of a gadget that they won't invent for another six episodes)
5-Patterns of the soul
6-Ruling from the Tomb
7-The Rules of the Game
8-Appearances and other deceits (Bellboy uniforms introduced)
9-Racing the night (Bellboy uniform, clear continuity errors if the other episodes come first)
10-The Memory of War (Belboy - this introduces a major continuity error in that the crew discover a very handy gadget in this episoe that they used in Paterns of the soul)
11-The Needs of Earth (belboy)
12-Visitors from down the street (Bellboy)
13-Each night I dream of home. (Bellboy)
There's also a continuity error in an episode in which the Excalubur fights the Drakh (I'm blanking on which one it is) and Gideon says, "Well, we've finally met the Drakh." But of course they already met 'em in "War Zone."
In any event, I think "Tomb," "Home" and "Game" are the correct order for the Lochley appearances, in that they follow a logical progression for their relationship:
1) They meet on neutral ground (Mars)
2) They meet on Gideon's turf (Excalibur)
3) They meet on Lochley's turf (B5)
