2003 Toyota Corolla Possible Rod Knocking

Let me start by saying that I know nothing about cars and I'm just looking for some help from someone uninvolved. The timing chain on my 2003 Corolla broke while driving this February. I had my car towed to a repair shop, who replaced the timing chain, tensioner, the water pump, and gears which they said broke also. After all these costly repairs, they let me know that there were valves in my engine that were bent and this meant my car would have to have a new engine. My father found a "good" used engine with about 70,000 miles on it and had it installed. The used engine came with a thirty day warranty from the day of purchase. The motor was installed by a friend of my dad's and because he works full time, this took about two weeks. Before I got my car back, my dad also replaced brakes, rotors, wheel bearings, and every little thing else that needed repaired, so the warranty was gone before I got to drive my car at all. The first day I drove it, the check engine light came on. The car had an obvious miss and no power at all. I took it to a local auto parts store and was told there was a third cylinder missfire. On the way home from there, there was a very loud pecking noise coming from the engine, which my husband says is a rod knocking, which means the engine that is in my car will have to be replaced. It still runs, but sounds horrible and since I don't want to end up broke down on the side of the road in the middle of the night again, it is parked. I would just like to know what may be causing this and how to fix it. I do not want to sink a lot more money into this car, since I have put over $3000 in it already and it still isn't driveable. Can my engine be rebuilt or repaired instead of being replaced? Should I take my car to someone besides my father or my husband and get a professional opinion or does it sound like they are right about what is wrong? I really don't know what to do!