knocking

I have a 94 Escort with 1.9 and manual transmission.
The original engine had about 180K when it recently died. I started it up one evening and there was a terrible knocking sound, which I later found to be due to the valve seats dropping.
I purchased a brand new rebuild and swapped the engines with no problem. However, shortly after starting up the new engine the same knocking sound reoccured! Fortunately my money was not wasted in buying the new engine, but it seems that something else was causing the knocking in the first place.
The only parts from the old engine to transfer over to the new engine are the intake and exhaust manifolds, as well as the injection system, coil pack, oil pan, and accessories such as power steering pump, alternator, and the like.
For the life of me, I can not figure what may be causing the knocking. It is possible that the new engine was not assembled correctly, but I purchased it fro ma very reputable company and I know the engine was tested before it was shipped to me.
It I used a stethoscope and can tell the noise is loudest near the front of the engine, somewhere around the #1 cylinder or the water pump (the pump is new). I can hear the knocking clearly through the intake and exhaust manifolds, but I assume that is just echo.
Also, the check engine light is on. The only trouble code I can get from the computer is 111, which is the OK code. It is my understanding that the check engine light is mainly related to fuel and emissions sensors, but with the OK code I don't know where to look.

So my question is this... knowing that it is a new engine and the few parts that were transferred, can anyone suggest what my problem might be?

My best guess is something with the injection system, but all 4 injectors sound the same. I have probed the engine thoroughly with the stethoscope and for all I can tell the moving parts inside the head and the block are functioning normally. If anything, it is related to something on the front of the engine, but all thsoe parts are new.
I have also checked the timing and it is correct.
Thanks for any ideas.

have you taken the aux belt off to see if knock goes.?

Turns out that when the valve seats dropped in the old engine, small bits of metal had made their way up into the intake manifold. When I fired up the new engine those small pieces were sucked right down into the new motor and caused the same tapping sound. I had to remove the head and clean it out again, as well as give the intake a good bath. All is well now... but I have to figure out how to get the check engine light to go away... it is a new engine so I suppose it will go away on its own after awhile... we'll see.