The center pull bridge thing, yes, that's your new cable stop. If you think about it, it has to be there now, or else your brakes will slacken when the shock compresses. You'll just need a longer cable housing, five bucks at your local shop.
I'm assuming you have cantilevers, not v-brakes. If you've got v-brakes, ignore the cable stop and run the cable the way it was.
I'm not sure what you mean by the springs not lining up, but I suspect you mean the hole for the thin wire spring doesn't meet your brake arm when you put it on. It shouldn't - you need to stick it on so the end of the wire goes in the hole, then swing the brake arm up, compressing the spring. That's what makes the brake pad to come off the rim when you let go of the brake lever.
Does that help?