D16z6, rebuilt bearings, rings, headgasket, and headstuds. Put 100 break in miles on it so far, babying it.

The motor was rebuilt because it blew a head gasket, and since I had everything apart I would replace and upgrade internals planning for boost. It was a good running engine other than the headgasket.

After the rebuild, ocasionally get a faint sound very similar to rod knock on startup, only for 2 seconds or less. Can't pinppoint, and it isn't every startup, nor is it only on cold starts or while engine warmed.

Last night I thought I was beginning to hear it also while driving, but could not tell, so I was playing with the throttle and gears to try and see. Could not tell over the sound of the exhaust and other road noises.

I get home, and while it's idling, I begin to remove spark wires one cylinder at a time to see if I can make any potential problems more prevalent per cylinder.
Cyl 1 (closest to the belts) removed just idles rough, so it seems it checks out.
Onto cylinder 2, car pretty much stalls right off the bat. This is the only wire removed. I go to restart the car, and it just cranks and cranks and cranks.

I'm wondering if the distributor took a dump coincidentally at the same time I removed the wire. The car should still run on 3 cylinders, right?

Anyways, not sure what else might be the problem, or what to check for.

Battery is good. Its new, no battery light, all dash lights work, headlights, and car cranks multiple times easily.

Fuel should be good, pump primes, guage reads 1/4 tank, and afr read between 13 and 15 on the wideband before stalling. Ive not had a problem with fuel before on the car, even running miles with the gas light on. So do not think this is the problem.

Air should be good unless the intake got clogged, but don't see how it could have that quick at once, with me standing there in the bay. It was not running bad just before, so it cant be a gradual clog.

Timing should be fine. Belt tension is good, and did not notice or hear it jump at all while doing the test

That leads to it being compression or spark.

I believe the compression to be good since it is newly rebuilt and has been running good the first 100 miles.

So last would be spark... I'm wondering if the distributor really did take a dump right at the moment I removed the spark wire, just coincidentally. Maybe that knock was the distributor gradually on its way out, missing sparks in 1 or more cyl for a split second? Weird because car seemed to be running fine, afr was good, seemed fine powerwise (or at least as much as I could while breaking it in).

Is there any way to test it before I start going around buying replacements, and is there anything else I can check to rule problems out?