1999 Honda Civic Ex Engine Knocking

My daily driver is a 1999 Honda Civic EX (D16Y8) manual transmission. Everything is stock except for an AEM short air intake. A few weeks ago, I threw a rod which put a hole in the block and had a friend of a friend put in another engine, the same model. I think it came from a scrap yard. I’m not certain of all the minor details but I did save myself a couple grand (that I didn’t have anyway) if I went though the Honda dealership. The original engine had around 168K miles on it, but the scrap yard engine had around 100K. I won’t be going back to this mechanic as there were several things not so good when I got my car back – the rubber seal that connects the air intake tube to the throttle body was bent back when it was clamped down so air was getting in. The power steering reservoir tank was basically empty but luckily I had some extra lying around to fill it. He left the top timing belt cover off by accident and told me he was too lazy to put it back on after bolting the valve cover on. Last and worst of all, he told me he couldn’t get the timing right between the camshaft and crankshaft. The mechanic did install a new timing belt and water pump. The engine is knocking, but it sounds more like a ticking sound and my car also has very poor idle problems – it will stall out almost every time I stop the car. I did remove the IAC valve and there was a lot of carbon build up which I cleaned out with brake parts cleaner. Didn’t make any noticeable difference. This engine does not have a FIT valve.

Note that none of these issues were happening and no CEL before this engine was put in.

Check engine light is on. I took it to Advance Auto Parts and had them hook up the code reader and I also did this manually this evening by shorting out the ECU service connector. The codes I am getting are 23 (Knock Sensor), 41 (Primary Oxygen Sensor – Heater), 71, 72, 73 (Cylinder 1, 2 & 3 misfire).

The ticking sound: it only occurs when I accelerate. On cold start, it won’t start ticking for a couple of miles when it warms up. It won’t tick when I just barely touch the gas, but the more gas I give it and the more load it has, it is more prominent. At higher RPM’s, roughly around 3,500 and up, the ticking gets very quiet and is pretty non-existent so I drive now at higher rpm’s than usual and give as little gas as possible so it doesn’t make the sound until I fix it myself.

If the timing between the cam and crank is actually off, I wonder if that is causing the ticking sound and misfires? The car doesn’t seem to run poorly enough to really notice compared to my previous engine. The plan tomorrow is to take off the crankshaft pulley and check the timing marks to see if it really isn’t lined up correctly and correct it if it is. I plan on testing the O2 sensor and replacing it this upcoming weekend, maybe that will fix the idle issue. The spark plugs, wires, distributor cap, rotor are about a year and a half old. I will check those out tomorrow.

Anyway, I am still a novice with cars. I have only really been learning this past year doing all of my own maintenance and it is beginning to become an addiction. Thanks to Eric and all his videos I have learned a lot and I have overloaded my brain today about timing belts and valve assembly. I think I am going in the right direction with this problem but any advice would be great. I will try to get a video of the sound it’s making tomorrow and as well as an update on the timing gears alignment. I really want to get a good diagnosis going of the issues before I start throwing money and parts at it.