1. There's no guide, sorry. Theoretically you could have a look at the mod's "universetextstextsdev_***.ini" files and look for the names presented in the Skirmisher (e.g. "weap_r_eshell") and get the ingame name and description from there, if available. That's a rather cumbersome method, though, but it's pure trial and error otherwise, I fear. In the default "NEXUS Skirmisher" mod there is a vague naming convention, though. For example, you might have "weap_r_eshell", which translates to "weapon, raptor, energy shell" - first comes the device type (weap for weapon, shld for shield, etc.), then a single letter for the alien race that uses that weapon (r for raptor, v for vardrag, g for ghost, etc.) and afterwards the weapon's name (eshell, ebomb, flak, etc.). At least that might give you a clue about the kind of device you're dealing with.
2. What devices specifically and which mod? I just tested the energy bomb (weap_ebomb) and it was working fine. As for the lack of jump drives: they're simply not included in the NEXUS Skirmisher mod, because it uses the default Nexus multiplayer ship classes, which aren't set up to equip jump drives or interplanetary drives. At least for the latter one it's an easy fix, though... open up "universetacticstacticstypes.ini" in your mod's folder (default: "modsNEXUS Skirmisher") and search for the shipclass you want to add an IP drive to. Look for one of the "Slots" lines of that class and append the number 81 to that list of numbers. For example:
change
Slots 61 61 61/65/67 61/65/67 61/65/67 66 66 66 66 66 66 ;
to
Slots 61 61 61/65/67 61/65/67 61/65/67 66 66 66 66 66 66 81 ;
If you're going to record machinima, however, you might want to learn scripting your own missions, though. Nexus has a rather comprehensive modding manual included and for everything else there's this forum
3. Not with the Skirmisher, but you can start the Nexus modding tools (should come with the game) and load the Skirmisher-created mission using that. There you can relocate and rotate every ship the Skirmisher placed there.