I have a 1999 Ford Taurus. I have noticed a faint knocking sound for about 6 months. I took it in and thr mechanic said ’ what noise? '. Then it got louder so I took ot back in and he ssid ‘bad water pump’ I had another mechanic friend check, and he said the water pump was fine. Plus, I’ve never had any overheating . a 3rd mechanic said “could be loose torque converter bolts.” It sounds like metal clunking on metal under the hood… rpms, speed, & temperature make no difference. Occasionally get a smell of coolant inside the cabin . I’ll attach audio of the noise.
You could remove serp belt as test and run motor. Not for long since wp is not turning. Does sound go away? Change? No accessory driven components will make motor run quieter for sure. Than u can see if u have deeper, bad knock sounds.
Well…website won’t let me attach audio.
The nlise is a faint knocking. .Always been there. .even after I got a new engine put in by a mechanic for a different reason…occasionally now I hear something that sounds like a belt not moving, but I checked qnd they are all moving .
Just looking for a few ideas to take to a mechanic so they don’t ty to make something up
It could be either the valve train or a bad connecting rod bearing. Find a mechanic who knows how to use a stethoscope. He should be able to tell whether the knock is in the top end (valve train) or bottom end (connecting rod). Also have the oil pressure checked. Low oil pressure means the engine is experiencing excessive wear and a bad connecting rod bearing is more likely.
Have the guy look for a cracked flex plate
A good independent mechanic with a lot of experience and a good stethoscope like @jesmed1 suggested is probably your best bet for finding the real cause of the noise. There are a lot of different noises in an engine…some good and some bad. It took several hours, years ago, to find a slight knocking noise in my Chevy pickup. It turned out to be a loose wrist pin in one of my cylinders. I drove that truck for about 5 more years without any problems.
“…rpms, speed, & temperature make no difference.”
The spring belt tensioner can make odd metal-on-metal noises.
You refer to a new engine being installed. Could it be assumed that this new engine is actually a used one?
The possibility of a rod bearing rap is there as one never knows the history behind used engines. I’m also aware that anything a salvage yard sells is always “guaranteed good”. They state this on every part they sell even though they have no direct knowledge as to whether it good or not.
Since it made the noise with the other engine also I would bet that the noise isnt coming from the engine. Usually when they replace an engine they reuse parts from the old engine, parts like the starter,alternator,etc. I bet its one of the reused components that is making the noise.
you said rpms and speed have no effect on the noise, so im trying to think what moving part remains at the same speed regardless of how fast the engine is running or how fast the car is moving.
I’m inclined to agree with tardrex that since it was present before the engine swap it’s safe to rule out the engine as a source, with the exception of the peripheral components as tardrex mentioned.
It might be as simple as a loose heat shield or exhaust component. Are you able to put the car on ramps and slide under with a good worklight? If so, make sure the car is safe and secure on the ramps and try shaking a few parts underneath. Go overboard on the “safe” part, chocking the wheels, making sure the engine is off, the parking brake firmly engaged, and the car on a solid, level, paved or concreted piece of terra-firma.
Maybe the possibility exists that both the old and “new” engines have rod knocks.
Pessimist. 
My wife says the same thing but I consider myself to be more of a cynical realist due to the track record of cars and especially used parts if that is the case here…
rod knox?
Well. .3 mechanics later 2 say it IS the water pump going bad. I guess it explains the coolant smell and the clunking noise. .but not why it hasn’t overheated ever… even on a 200 mile trip I took recently before the noise was very loud.
So ill put in the pump and see what happens I guess.