Series 1 misfire on rotor 1
 

I've been chasing this misfire for a week now. It pops up at about 4k rpm on rotor 1, and it seems to be a wiring issue. I was trying to get it to move to rotor 2 by moving things. I rotated the coils, plugs, wires, and injectors one by one, starting each time, and it misfired on rotor 1 each time. Any help on where to start looking for shorts/ wiring issues would be extremely helpful. thanks guys :)

How's the catalytic converter? I'd look there first. Since you rotated the coils and plugs, that would seem to indicate it's not an easily accessible wiring problem, if at all. Eliminate the easy stuff first.

I hadn't thought of the cat, the seller I purchased it from said it had a new one so I haven't checked it. How do I go about doing that?

Wait for the car to cool.
Lift the passenger side and support it with jack stands.
Remove the three bolts connecting the exhaust manifold outlet to the front of the cat.
Gently pull it down a few inches and shine a light in there. See if it looks like a very fine honeycomb, mesh, or spiral. If it looks like chunks are broken off or it's folded in on itself, your cat is hosed.
Maybe post a photo here.

oh god I installed that with a load of exhaust sealer and the old gasket since I couldn't find a new gasket locally

Yah, that's not going to last. Even Permatex Ultra Copper won't hold up against rotary heat.
If you used too much of the stuff, it might be causing some of your problems. Get the proper gasket and scrape all of that crap off of the mating surfaces.

It wasn't a ton, just put a layer on the mating surfaces. I'll update the thread once I check the cat

It would also be good to get OBD data on airflow and fuel trims on a warm idle (and warm idle only). If the cat is fine, you have an array of possible culprits from poor aftermarket intake to misbehaving injectors. Having data might help add supporting evidence for or against any of those.

And also also, from the "eliminate easy things first" opera, perform the 20-time brake pedal stomp procedure to reset the ESS profile. It's possible but a bit unlikely that it would cause a single rotor to misfire, but it's so easy to try that you'd be silly not to.

I'm not sure if I can get fuel trims with my scanner, but what should I look for? Also, what does the ESS profile do, as that might make some sense. I put a different engine in this car so maybe it's just not playing nice? I already tested the injectors by rotating them, and the misfire didn't move. I'll be testing with a noid light to check the wires, and the intake is stock. Thanks for the tip, I'll try it tomorrow. :)

If he installed a cheap cat it won't last if it's running fine, much less with misfires.
Bad cats can cause misfires, but you'd usually get a P0420 code.
If it is a cheap cat, you should take it off and install a midpipe.
If it's still good, you can save it for emissions testing if needed, unless you're in Cali.
If it's already bad, you can gut it until you get a decent pipe.
You should avoid running it with the cat while it's misfiring.
Misfires kill cats, bad cats kill engines.

Ah so you replaced the engine. Definitely do the 20-time brake stomp procedure (google it). Without getting into physics, your computer learns the behaviour of the ESS (crank position sensor for all intents and purposes), so if you change the engine, including a different ESS, you need to force it to relearn the new sensor. Hence the 20-time brake thing, it's the secret code to clear non-volatile memory and force a relearn.

Issue fixed!
 

It was the ess after all, It runs so much smoother now, and throttle response is improved. Most of all, no more misfire! Thanks for all the help, guys.

Good news, thanks for the update.
:)
Don't forget to look into your cat situation.