Engine Knocking

The car starts up fine, but there is a knocking noise. You notice it the most when you accelerate, or when you slow down. I just changed one set of connecting rod bearings. The crankshaft looked smooth still, with no noticeable damage, and the other bearings were also still good. But now, after you drive the car for about 20 minutes, it seems like one of the cylinders stops firing. If you shut it off for a little while, maybe ten minutes, that problem stop, but it will come back. When itd does that, the check engine light flashes. At first I thought it was the spark plug, and I changed them, but it didnt help. Then I thought it could be the coil packs, but they seem fine. I know its not the oil. Honda recomends 5W-20, and that is all that I use. I am going to do a compression check, hopefully that will give some answers, but does anyone have a good idea of that I should be looking for? Also, sometimes when I start it, and when it idles, it will want to die.