Let me start by saying I hate rigging. A lot.
So, fun part. I made the rookie mistake of making each set of bones a separate armature. Yay.
This leads to special problems when I try to join them into one armature. Yes, I know, CTRL+J. Great. Doesn’t work right. Trying to merge armatures rotates one of them, no matter which armatures are chosen.
BONUS ROUND:
So, since I hate rigging, I also seem to have created another scenario that I can’t figure out how to work. The character has armor (not included in .blend), but she’s on a mirror modifier. So, I can’t select the armor for the shoulders or the bracers on both sides to set the weight paint, just one. How do I get around this? Or am I asking a dumb question with a nonexistent problem that I don’t know doesn’t exist because I haven’t started weight painting yet?
I’m at work so I can’t check the file itself, but check that each armature has no rotation applied to it in object mode (apply rotation etc), and see if that fixes joining.
For painting weights with the mirror modifier, it will intelligently mirror weights provided a destination group exists. So, if you say create a shoulder.L and shoulder.R group on the should armour, and then assign all the left verts to the .L group, the mirror modifier should assign the mirrored verts to the right group.
Also check the bones and “normalised” before you join the armatures, if you indeed need to do this. It would be a good idea for you to read the manual pages on bone normalising - there’s not too much and it can be very useful to you.