You say I'd need to make a "shields up" sprite for each ship, but the blue glow that goes with it comes on automatically? Is it possible to change the colour of the blue glow? Also, to make it completely accurate, the shields would need to be an oval around the ships, not conforming like yours. Is that possible? I mean, given the choice between vanilla shields and conforming, I'd pick conforming, but it's not entirely accurate.
As to your technical difficulties - I really do not understand most of what you're saying. But what comes across is, using it as a system ID prevents weapons fire whilst shields are up, but you can't make shields act like this. Currently, the available shield options are Omni, Front, Phase and None. Could you not add another shield type in there, that uses the code you made? In the same way as you'd just insert a new planet, or a new engine type?