Did you ever replace the spark plugs? Obviously they have to be fouled if its missing. You did change the distributor, so check your plugs. Replace them and make sure they are gapped to Honda's spec. Once that is done, IF it is still mis-firing, take all the plugs out and put a long straw into cylinder #1 or cylinder #4. Spin the crank until the pistons in cylinder #1 and #4 are at top dead center (TDC). The straw should be sticking up and out as high as it possibly can, just make sure the straw is actually ontop of the piston. once it is at TDC, take the distributor cap off and make sure the rotor is pointing right at the spot where the cylinder #1 plug wire is applied onto the distributor. Once that is correct, make sure your cam gear arrow is pointing directly up. If its dead on, than your timing isnt your problem.
Since there are no CEL's, than your sensors aren't the problem either(electrical). So what does that leave us with....? Could be a problem with the ecu... most likely not, but swap another ecu (stock for your engine/harness) and see how it works than.