Going on memory, code for forgive me as I'm guessing without looking, doesn't the OBD-II use a knock sensor........trace that from the PCM/ECU to the engine and see if they wired that in as well.

 

Did you ever figure this out?

I put a 94 f22b1 with low miles into my 1997 accord ex.

i used the 94 engine, harness and distributor.
getting the same misfire codes you mention.

P0301, P0302, p0303,p0304, p1300, p1399
For me these codes only pop up with highway driving. The car is very smooth driving it. Not like misfires i’ve had before. Like you said it seems like a false misfire. Althoigh once the CEL comes on, the car does have a lumpy idle when placed in park. But only when the codes are present.

I tested the wires to the firewall connections. For 94 vs. 97 the cyp, ckp and tdc are in the same locations at the 3 plugs near the fuse box. The only other difference in the two harnesses i can find is that 94 had the vtec oil pressure wire (blm/blue) and FIA wiring near the injectors (wht/yel, blk/yel)

So far i have tried swapping plugs, plug wires, egr, dist cap and rotor. Tested wires for cyp, ckp, tdc. Tested iacv wires.

I thought about installing the 97 harness and hardwiring the 94 dist. Seems pointless though since thats what you had with the same codes.
Also wondering if there is a shared ground somewhere or other wire that is open.