That's a long and involved question, do you have a few weeks? 
I'll try and recall bits from the top of my head, but might have to come back later.
First off, when working with coordinates of weapons, they apply to positions in the LOW RES version of the BIF. Each weapon is identified by its top left and bottom right corner in the file and they are all defined in the Textures/Men/[BIF plate]/Weapons.txt file
I'll use an example from the vanilla game, as that's what I've got loaded on this machine (but won't run it.... the other machine does....)
Look at Textures/Men/Burnous/Weapons.txt and you'll see this:
Code:
1,239,64,246,2,1
145,244,187,247,1,1
91,248,187,250,3,1
58,252,187,254,2,1
208,246,255,254,1,2
58,252,187,254,3,1
These are weapons numbered 1 to 6. In each line the entries are x1, y1, x2, y2, length and width. x1 and y1 are the co-ordinates of the top left of the weapon, and I'm sure you're up to speed enough to figure x2 and y2 from that. These are pixel numbers. In ReadBIF if you hover the pointer over tool over the BIF plate (low res, remember) you can read out the pixel coordinates on the right hand panel somewhere. We can forget the length and width for a while, as they scale the weapon (ie an axe can be a hand axe or a big two-hander or a polearm by stretching or squeezing these values; likewise a spear can become a pike.... but I'm getting way ahead of myself here). But you can see weapon 4 and 6 in this list have the same x, y coordinates, but different length/width values. They are basically two different projections drawn from the same image but at different scale.
Shields are defined in a similar manner, but differently:
See Textures/Men/Burnous/Shields.txt
Code:
189,218,205,254
115,222,140,247
Obviously shield 1 and shield 2. These are defined simply by the corners, no length or width, because they are realised differently in BIF.
When setting the actions in ReadBIF, you have to input the weapons' rear and front coordinates. If the length is given as two in weapons.txt, the weapon will extend beyond the front coordinate to twice the indicated length, so for a spear you generally need to place the 'front' of the weapon at HALF WAY to where you want to extend it to. For weapons like swords the 'rear' coordinate obviously needs to coincide with the hand. Spears usually need to sit behind the hand to look normal.
Now you might begin to realise how long-winded it is to set up these coordinates. For every angle, in every action, in every one of the twelve plates in the BIF you will need an entry in the actions file.
My WIFI keeps dropping out so I'll have to split this up....
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