2005 Honda Civic D17A Automatic 260,000km

Recently over heated (pin hole in rad neck)
Replaced Rad
Checked flatness of block and head (within spec)
Replaced Head Gasket

Now I see a few misses at idle on cylinder 4 (I might see 40 if I let it idle for 5 min)
Once the engine gets above 800rpm, they completely disappear.
No codes are being thrown, and readings on obd scanner all look normal.
I cleaned the IACV valve and did an idle relearn. No change
I swapped coils with a different cylinder. No change.

Next steps:

1. Check compression
2. Swap spark plug with another cylinder

What else should be on my list?

Valve lash

Would that change from doing the head gasket? or just a coincidence?

No clue, just something that you can check that might have an effect on what's going on

It helps if you are looking at cylinder 4... not cylinder 1

As soon as I looked at the coil, I could see some damage (it looked melted).

When I moved it to cylinder 3 the misses followed.

I replaced the coil and all seems to be working properly

Glad you figured it out