About a month ago I began hearing rattling noises when I would depress the clutch. Over a few days the noise became less noticeable but then I started having trouble shifting gears (5 speed manual transmission ford ranger 2002). It was first diagnosed as a leaky master cylinder and that was fixed. The truck drove fine for a couple of days and then the difficulty returned to the point where I could not drive the truck at all. Then it was diagnosed as the input shaft, that was a week ago. Today I'm told I can pick up the truck and oh, by the way, it wasn't the input shaft, they put in a transmission???? Do I trust this third attempt to resolve the problem? What would it be about the transmission, that it would need to be replaced?

resonance at rpm when stationary can only come from those parts rotating
That limits the noise source down to the engine and transmission
Starting with the engine , the most obvious noise sources are the idler pulley bearings , water pump bearings , power steering pump, ac compressor pulley bearings (compressor if activated), drive belt-loose or failing and harmonic balancer rubber failing
There may be a noise source from a worn/loose timing chain and that noise will be as a harmonic rattle
moving on to the transmission
If manual , bearing noise can be determined by the application of the clutch
Throw out bearing noise will stop or get worse with the clutch depressed and gear /bearing noise will stop with the clutch depressed
Probably not a lot of help as the description of resonance is wide open to harmonic--rattle , whirring, hum or even loose material in the exhaust system such as failed cat converter moving around

Whenever you hear a tap, rattle or thumping noise take to a mechanic or someone who knows cars you do not want to blow a rod through the block. It could be starting to freeze take it in!

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Bearing noises in a clutch system are easily distinguished by running a few simple tests. Start the engine and leave the transmission in neutral. If a transmission makes noise when it is in neutral it is often a worn input shaft bearing. Now depress the pedal until the clutch just engages. This is the point where the release bearing is just contacting the pressure plate fingers. If you begin to hear a squealing sound this is likely a worn release bearing. If a whirling noise is present when the clutch pedal is fully depressed it is probably the pilot bearing.

Could be catalytic con.in side.

If it goes away when you depress the clutch it is most probably the throw out bearing-if it were related to the crank or rear main bearing you would hear it all the time.

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Check the heat shield over your catalytic converter, see if it's loose.

I would be suspect of bearings or CV joints, but first look at balancing tires. they would be able to tell you if the others are due for repair.

If you notice a change in the rattle,when you depress the clutch pedal it is most likely in the clutch,or the linkage.The release bearing will most often have a squeal or a hissing sound.The clutch fork can rattle, if the ball pivot retainer is broken.You may feel some unwanted slack in the clutch opperation,and you may be able to adjust this out,but maybe not, with a hydraulic clutch.

This is more than likely an input cluster bearing beginning to fail. It could also be a sign that the gearbox is simply out of oil. Check oil level & if it is ok it is more than likely the input cluster bearing in the gearbox. Low oil is usually accompanied by gear noise which is usually more noticeable in 1st, 2nd & reverse. Input cluster noise is much less noticeable when in gear due to load on input shaft.