After doing a few of these kits for timing sets at this point, I can confirm the initial alignment is where you'll have everything line up perfectly. Unless of course you're lucky and happen to hit the magical revolution where they line up again (some amount of math can figure this out, but certainly not a number you would hand crank over to). If it did line up at first glance, I'd buy a lottery ticket. If you don't trust it, you can always go through the motions of taking it apart as if you had a new set, and re-installing it (also learned this a few times too).
But really though, this build is one of the more solid ones. It's odd to just be all of a sudden dead. The following may seem like dumb thoughts, but certainly back to the basics:
- Are you running enough/the right fuel? Sounds like a yes on enough fuel from reading, but state to state can vary with octane levels and additives for summer/winter gas, so could come down to a touchy tune and a recent refill that the car doesn't like.
- Are you getting airflow? Again sounds like yes, so probably not anything here unless it's a MAF/MAP sensor that you'd see with a code scanner. Those can go all of a sudden.
- Are all your electrical connections secure? This one was interesting only because you also mentioned a bad battery too and there's always room for a current draw somewhere. Again, wouldn't expect given the build history, but you never know.
I have to hand it to you, you're well into this project already for getting it recently and already having the engine apart. You'll find that ah-ha moment soon, and get to learn a lot about the build you now own while you're at it!