Engine knock?

Hello, I'm a mechanic at an independent shop and I recently took over someone else's job because they quit. The other mechanic had a rear main seal to replace and an oil pan gasket to replace and valve cover gaskets to replace. He also had exhaust gaskets to replace but did not notice that the exhaust stud was broken in the left cylinder head. So, my problem is, is that this broken exhaust stud on the driver's side in the back next to the firewall was not accessible with an angle drill. So, I removed the cylinder head and drilled out the stud and re-tapped it and proceeded by installing a new head gasket, exhaust gasket, and new intake manifold gaskets. After the repairs were done I started the vehicle and noticed a bad knocking noise coming from the back of the engine. I thought maybe I've done something wrong so I removed the valve cover to see if maybe the push rods were put in wrong, but they are all the same size and in perfect condition, reinstalled the components and started the vehicle again and noise is still there. So, I started thinking that maybe the other tech may have installed/or not installed something wrong to cause this problem. So, my question is, could putting on a new head gasket cause this problem because not the one side has better compression that the other side?