Ford Mustang makes whining noise?

Please no ford jokes lol. My 11' Mustang gt (manual) makes a whining noise when accelerating and it started in the beginning of winter about 4 months ago. Recently it's been getting worse. I notice when I push the clutch in the noise cuts out immediately as it goes to neutral. When I'm in 5th and 6th year it's at its quitest and 1st is the loudest. It seems to whine with the rpms so the higher the louder. I heard it's something with the transmission. Could it be something else? Check engine light is also on but it says it's something minor. Not sure if it's related. Any opinion is appreciated.

When was the clutch last adjusted? Replaced? Those are the 1st things to look at… And as for the check engine light - it's possible it's NOT a minor item! Time to have the code(s) shown on an OBD reader and see what's really going on

The transmission needs to be dropped to get a proper diagnosis. Could be a bad clutch fork pivot ball/bearing (inexpensive fix) to a bad input shaft bearing (not good news).

That is in the transmission. When you depress the clutch it disengages the transmission from the engine and the transmission stops spinning. Meanwhile the pilot bearing and clutch release/throw out bearing are running at the speed of the engine. Very easy diagnosis if you can picture what's in there and what it's doing.

On many transmissions I've found a heavily worn bearing on the input shaft, the front bearing in the trans. Meanwhile the rest looks good so I've just replaced that bearing only. I think it's installed from the inside on your trans so not an unskilled task.
Look for recommendations for a different fluid for the trans too. Syncromesh and gear oil mix seems to make people happy. NOTE really thick oil, like gear oil, in cold places will have a hard time reaching the bearing and it will run dry until trans warms up ruining bearing. What is in the trans now? People mistakenly fill gearboxs with gear oil often.

Check the muffler bearings and shock bands. The muffler bearings should be greased with dry water at all times and the shock bands shouldn't be hanging off the wheel thermostat.

The reason Ford's and people who own them are picked on: The vehicle makes no sense, and in most cases people who own them have no common sense. Your question is a prime example.
One of the problems is on top of the drivers seat between the wheel and back of the seat. Another problem is both on the front grill and rear of the vehicle, it's a blue symbol with an F word in it but the main problem with this F word is, you've been told correctly, something with the transmission.

Apply some common sense even if you are not knowledgeable on how cars work. When you stop using the transmission the sound stops, right? So the problem isn't the sunroof or windows.

Check the fluid level in the transmission and quality of the fluid. If it's black or an extremely dark red color and smells burnt it would probably be helpful to have the transmission serviced meaning have the screen and fluid in the transmission changed. This generally costs around $200 to have done and it's basically the same thing as having the oil changed. The screen in a transmission is what an oil filter is to an engine and the transmission fluid is lubricant for the transmission like oil is lubricant to the engine. It's not often that these things need to be changed in a transmission but it does need to be done now and then.

Some vehicles no matter their make or model can't have their transmission fluid level and quality checked by the owner because (for reasons beyond me) they no longer include a dipstick to check it with. They cap the dipstick tube off in newer vehicles so it has to be taken to a shop to have the transmission fluid and quality checked.

It's not going to hurt anything to add a half of a quart of transmission fluid to it and see if that helps. At a guess, which may not be anywhere near accurate because I'm not there in person to look at it and hear it for myself, I'm guessing this noise is because it's low on transmission fluid.

It's in your best interest to take it to a garage as soon as possible. A mechanic ALWAYS looks at and wants to hear noises themselves to give a free evaluation as to what it might be and then he/she can give you a 'round about estimate of what it's going to cost to fix.

With this kind of thing going on you may have already left it go too long and it's caused major damage that could have been prevented if you got it taken care of right away. If it's getting worse it's going to keep getting worse until the tranmission just plain stops working so don't let it go any longer.

You have a bad input shaft bearing in the transmission.