Well, rats! 'Good thing I didn't bet a nickel on my own advice.
Hmmm. Yes, everything looks o.k. in that area. No signs of scraping or metal-to-metal contact. That's a good thing - and a bad thing. Good thing is, this is not the cause of the knocking. Bad news is - you still need to find the source of the knock.
So far, you have eliminated the most common causes of knocking when the clutch pedal is depressed: (1) cocked ring gear; (2) crankshaft bolt heads too tall; (3) clutch disk hub too thick. Let's look elsewhere for a moment.
You mentioned in your original post that the knocking continued even after releasing the clutch pedal, but there's no knocking when hand-cranking or using the starter. Is that still correct? If so, then we might be on the wrong track by suspecting the clutch area. I refer to the knock still being present even when the clutch pedal has been released. Are we correct that you for sure isolated the knocking sound as coming from the clutch area? Remember that noise emanating in the drive train telegraphs through the whole car so that a noise in the rear end can sound as if it's inside the transmission.
You also mentioned that this is a new engine. Was the engine block top decked and was it bored oversize, like to 0.100"? If so, it's possible that the top of the block has been decked before and now the tops of the pistons are slightly protruding above the surface of the block and are striking the edges of the head gasket, which in some gaskets overhangs slightly into the cylinders because the gasket holes are not large enough. This becomes more of a problem with the bigger bores, say 0.100" and 0.125" and is more commonly seen among older repo head gaskets than the newer ones. It might be that only one cylinder has this problem for some reason, which would explain why you hear the noise once per revolution. If the gasket is the problem, eventually the overhang into the cylinder will burn away and the knock will stop. Kind of unnerving in the meantime, though.
To re-assure yourself that the repo crankshaft bolt shanks are not too long and striking the rear main cap, remove one bolt and compare it to an original one, or post the measurement so that we can compare. I should think if the bolts were too long, it would lock up the crankshaft. Examine the tip of the bolt you remove for signs of it clipping the rear main cap.
Also, use a pry bar against the pulley to see if the crankshaft has fore and aft movement. This is only supposed to be about .005" endplay allowed. If radically more, the crankshaft could be moving forward and striking the back of the rear main cap, especially when the clutch pedal is depressed. That moves the crankshaft forward a bit anyway. Too much endplay slop would only make matters worse, especially if the bolts happen to be just a smidge too long. Hand cranking or even using the starter wouldn't re-create the knock. Try holding the clutch pedal all the way in and then use the starter. If you hear knocking then, the crankshaft is moving too far and/or the bolt shanks are too long.
Anyway, check these suggestions out next before we panic.
Marshall