I think Ive decided on the SE with electronics, and not the Custom, because It seems to be of the same quality, save the wood types, and is $100 cheaper.
If anyone knows something I dont about the differences between the SE w/Electronics and the custom, Im all ears.
Let's be absolutely clear what models we're talking about here. The SE Angelus comes in two flavors: Standard and Custom. Each of those versions is available with or without electronics, for a total of four distinct models.
I'm assuming you're only looking at the Standard with electronics vs. the Custom with electronics, since you stated that you're playing live with amplification.
The differences between the Standard and the Custom are only the types of wood used. The Standard has a Mahogany back and sides, and a Rosewood fretboard and bridge. The Custom has a Rosewood back and sides, and an Ebony fretboard and bridge. Both have a mahogany neck and a spruce top.
There is an audible difference between the two. Which one you prefer is a matter of taste. The Custom is a little more expensive, yes, because of the tonewoods. That doesn't necessarily make it better -- I personally prefer the Standard -- but I will note that most people prefer the sound of Rosewood back/sides.
You were originally comparing against the Taylor 214ce, yes? That's got a rosewood back and sides, so the Custom is probably a closer comparison than the Standard. But as I mentioned, I personally prefer the Standard; it's got a more pronounced midrange, and responds really well to adjustments in pick attack, whereas the Custom has a wider tonal spectrum, so it's more balanced with sparkling highs and deeper lows.
It's really just a matter of which sound you like. The best video I've seen for comparison is this one:
It's in Thai, but they demo each guitar at the end, so you can get an idea of what the tonal differences are like. I recommend using some good headphones or speakers to listen to it; laptop speakers aren't going to convey the tonal subtleties here.