Issue #1: Trace all your wiring, make sure everything is correct. A nice multimeter will be your friend for your 240. Also I wouldn't trust Autozone tests.
Issue #2.1: Make sure the injectors are plugged in proper order. Is it misfiring at all RPMs? I know people swear by soapy water, but build/buy yourself a vacuum tester. Will help you further down the line as well. Vacuum leaks can be culprit of a lot of different issues. Vacuum leak could very well affect your braking issue as well.
Route the vacuum/pcv system back to oem spec. Venting to atmosphere has no benefits.
Issue 2.2#: Also listen while car is running if you hear any whistling coming from brake booster area, and/or test the brake booster. Remove the hose to the brake booster and plug it. The brakes will be pretty hard to press. But if it was leaking and you plugged the vacuum line going to it then it should clear up the problem. Don't drive it plugged.
Issue #3: Get the FSM, or wiring diagram for alternator, make sure wiring checks out for that as well. And judging from what you describe I would still guess the alternator is bad. Autozone testing, is still something I don't rely on.
Been awhile since I owned an SR, so these are just things from the top of my head. Hope it helps