Ok, I've done some more diagnosis on the engine and found the source for both noises within a good margin of confidence. The light tapping/clicking noise is due to a crack which has re-formed in the driver-side exhaust manifold. It had previously been brazed over as a temporary fix before the turbo manifolds were fabbed and installed. So that's the good news I suppose. Here are a few pictures of other potential sources of exhaust leakage, with the first two and last being known sources of leaks: driver's side manifold, the driver's side joint to the Y pipe (makes a dull muffled pulse, but not one that is easily ignored even from in the cab), and the joint from the y-pipe to the rest of the exhaust (lets out some of the motor's growl).
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The exhaust is not a strong point for this build ATM. It is a known temporary component and has not received much attention due to the redundancy of perfecting it. Don't worry, it's all going in favor of dual 2 1/2" stainless piping all the way back (with an x-pipe for the O2 sensor just below the passenger foot-well).

The other noise is more than likely a spun rod bearing on the #4 rod. This was determined by removing the spark wires systematically until the noise ceased. When I got to #4, the knocking under load went away, but the clicking persisted (makes sense). The test for the clicking was to unbolt the valve cover for the driver's side bank to see if the noise grew in volume when it was slightly lifted, while performing that test, I noticed the crack. The noise did not grow while the cover was lifted. Due to the shape of the intake I was unable to remove the valve cover entirely for inspection without a much more in-depth disassembly.

As for the cause of these problems, I still need to wait until I have the funds and time to actually fix the motor entirely to pull it apart for a more thorough investigation. Thanks as always guys for all the help on this project. It isn't dead, just on the back burner. More will come in the future, but I'll need to fix it first.