Strange sound coming from my 00.. Engine or something else?
 

2000 Miata Engine Noise? - YouTube

I am really having a hard time distinguishing where this sound is coming from. Could it be the engine or somewhere else?

Obviously as wishful thinking, I'd like to believe it's not the engine. I have no issues starting it up/driving it, and I get a very good mpg (if that even matters).

Before worrying too much, know that the BP engines were known to be sensitive to oil quality and would often make horrendous lifter knocks and ticks when the oil needed changing or when a higher detergent oil was required. I have no idea as to why, but it is common.

I use Rotella T6 synthetic oil (as do most of the turbo Miata track guys) because it is very high in detergent additives and contains better anti-wear agents than standard gasoline engine oils. It comes in a blue one gallon jug at the Advance Auto or Autozone stores. I would suggest changing the oil to a high detergent oil and see if that helps.

Wait. You have a 2000? That is a solid lifter engine and not a hydraulic lifter engine. You might be hearing any number of things. It could be lifter clearance being too great. If it has ever been overrevved due to a missed shift the rods can stretch and the pistons can hit the head or the piston can fail. A lifter shim can come out and leave you with way too much clearance. Oil starvation may cause rod knock, which is pretty bad.

I took it to a mechanic that was reccomended to me from another Miata forum. The noise was coming from the shims being off by a little. It did not get adjusted because they were so barely off that it didn't really make a difference. I did get my timing belt changed though.

So it was lifter noise? Good! That's no big deal.