Misfire at cruise, popping/afterfire at 3000RPM

Is this a new build, or did it just recently start misbehaving?

If it were me, I'd pull the valve covers and rockers shafts/pushrods. It wouldn't take long and would tell you real quick if something is fubar up top. I've seen issues like this before turn out to be a bad cam, bad rocker arms, failed lifters, etc. The issue being present when revving in neutral is what makes me suspect valvetrain.

These types of issues are often easy to spot with the valve covers off, and especially if you crank the motor over (with ignition disconnected!) and watch the rockers.
You could also set TDC on #1 and watch the springs as you remove the rocker shaft and see if any of the valves are being held open somehow. At any rate, lots to see and determine under those valve covers.

Not that anyone above is off the mark, but no amount of ignition fiddling will fix a mechanical problem, then again no amount of mechanical fiddling will fix an ignition problem either!
Well, I bought the car a few months ago, and according to the guy I bought it from, the engine has about 500 miles on it. He had the 440 built and dropped it in to replace a 318. He said he put some miles on it to break it in, but started having trouble tuning it. Got frustrated and pushed it into storage, where it sat for 20 years.

I'll pull the valve covers off today and have a look.

DO NOT TAP the valves with the piston parked at TDC!
Ok, at the top of the compression stroke you can, but be careful that you do not tap a valve deep enough to smash into a piston.....
To do a LD test, the piston has to be at the top of the bore, and on the compression stroke so that both valves are closed.
If you have a solid-lifter cam, there has to be at least some lash evident.
When you inject the air, it likes to blow the piston down, so; the piston has to be almost exactly at TDC. Furthermore, the LD test is usually done at a low enough pressure (30psi) that you can control that pressure surge.
I inject 80psi because it gives me a reasonably accurate result; but
I installed a valve on my tester that allows me to bring it in slowly, so the dang piston stays at the top. And my tester has only one gauge on it so that I only have one error to deal with.
So, then I deadhead my gauge, and adjust the regulator so it reads 80psi. Then without moving anything, I open my valve to exhaust the gauge, then slowly bring the pressure back up. If the piston moves, I back it up and start over. If the piston stays, then the gauge will read less than 80psi, because some of it always leaks somewhere.
So then, if the gauge reads say 76 psi, then the pressure loss is;
(80 less 76)/80= 5%LD

Had you tested with the typical 30psi;
then 5% would be (1 less 5%) x30=28.5psi. But most of us would not be able to read the .5 psi on the stinking little gauge supplied. Maybe not even a full psi. So we might round it to something like 28 or 29 psi and call it done. But 28psi is ;
(30 less 28)/30=6.7% LD, and
29 is; (30 less 29)/30= 3.3% LD
Both numbers of which are way out to lunch, compared to the correct number of 5%.

So the bottom line is to always test with as much pressure as you dare,
BUT
Always make sure there is NO BAR on the balancer to slam thru the rad, or smash your hand...
I am comfortable with 80psi, which, on a 4" piston, is 1005 pounds of downward force;
that's a lot of force.
If you ever can't unscrew your balancer-bolt, now you know the secret.......
30psi is 377pounds of force, a relatively tame-looking number, in comparison. Don't let it fool you; you cannot hang on to the bar very long after it starts moving; so I highly recommend that you don't even try..

To avoid all the rig-maroll,
you can unscrew the rocker shafts, and do the LD with the pistons anywhere; the pressure will push them to the bottom, and then the LD number will stabilize. With the pistons at the bottom, you can rap the valves to your hearts content.
My LD tester is a NOS Harbor Freight model - seems a bit better quality than the newer junk, but maybe it's just older junk...LOL. I like the idea of installing a valve to control the air flow. What I did was zero the test gauge at 30 psi and go from there. Once connected, I referred to the second gauge which shows leakage, and thats how I got my numbers.

Regarding the method of unscrewing the rocker shafts, help me understand. Wouldn't the air pressure also push the valves shut, causing a false reading? This seems like a much easier method since you don't have to fuss with finding TDC, I wonder why more people don't do it this way. I also may not understand what you mean...

Edit: When I tapped the valves, I tapped pretty lightly. Light enough to where I don't think I was even overcoming the springs. I just thought that maybe a little bit of energy would settle the valve, if that's what it needed. Hopefully that sets your mind at ease a little...haha.

I would replace the coil.
I have a newish MSD Blaster 2 that I had installed briefly, and while that may not be exactly when I noticed the problem, the problem definitely existed using that coil.