904 causing knocking noise?

If it comes and goes, theres good news. Its not bearings.At least not likely.
Again I ask, does the engine idle smoothly, and at a reasonable speed. The slanty is generally a very smooth running engine. But if yours is missing, bucking, and farting, then all kinds of things, attached to the engine,could be a possible source.
However, since you are convinced its internal, Im going to assume that you are right.
Since, Im convinced its not bearings, or pistons, or valve train, based on the comes and goes knock description, there are only a few things left. Again crank endplay is first on the list. Next would be; loose starter, broken fuel pump return spring,maybe a cracked flexplate.
BTW, what oil is circulating, and how did you determine that? It seems you are referring to engine oil, and I specifically asked about transmission fluid level. Are we on the same page?Going in/out of gear is usually the pump sucking air, whitch would be low oil level. Old Mopes are checked in Neutral,on level ground, oil hot, with correct dipstick.Put the park brake on or block the wheels from turning, or use common sense, to not let the car roll away, or worse, over you.

To check the crank endplay, its a simple matter of, with the engine off, and with suitable tools, prying the crank out of the motor towards the rad and then slamming it back in with muscle power.If it makes a very audible noise, that sounds eerily similar to the noise you heard in the running engine, well then, there you go. This noise originates deep within the engine, and has a very particular deep clunk type sound.Try it several times. No sound is good news.
The broken spring idea is a completely different sound. Its more of a clacking sound. The pump is hanging off the side of the motor right near the distributor.
The broken flexplate I cant remember the sound, as Ive only heard it once in my life.I cant help you with that.
I guess theres one other idea. If the oilpan had received a dent in just the right place, I suppose some part of the spinning crank assy could be tagging it now and then. But thats kind of a stretch. Only one way to know.Slide under it.Put your hand on the pan with the engine running.Youll feel it.Watch out for moving parts.And the hot exhaust.
In post 3, you switch from clunk to tap. Now we are no longer on the same page. So whitch is it? The above is for clunks, only. Taps is a new page.