Ave Alexandros Megas!

To answer your first question: yes, you can switch factions during a campaign by editing the script. See Hax Civil War guide for an explanation of how it works. Unfortunately, there are a couple of technical issues that may make it difficult to do what you have in mind. Firstly: you can only control a single faction at a time (i.e. you need to switch between factions rather than playing them both). When you press end turn, the other faction will be controlled by the A.I.

Secondly, the EB script (particularly the government system) hasn't been designed with faction-switching in mind. The script automatically places governments for A.I. factions, but the player is restricted by the "homeland" and "expansion" markers. These markers are placed at the start of the game. If you switch to a new faction, you'll still have the restrictions of your old faction.

So you can momentarily (for a turn or two) take control of another faction without much problems, but doing so frequently will take some effort. I am also not sure how effective it will be when A.I. Carthage and Rome decide to go to war. Chances are the A.I. will undo all your work the moment you resume control of the Seleucids.

On to your other questions:
1) Try the freeware version of FRAPS.
2) Should be possible, but I don't know how. Try asking Jirisys, or check the modding forum for how to alter the portraits.
3) Not as far as I am aware.
5) Yes, unfortunately. Specifically, there is a limit to how many models the R:TW engine accommodates. EB is at or near the limit, as many models are shared between units. There is another strange limitation of two* units per faction per model, so reusing models only gets you that far.

(* actually one, but you can use it a second time when a unit has the mercenary attribute.)