Clutch problems I can feel like a slight "pop" in the pedal

A little background here.

At approximately 200,000 miles, I did a full clutch replacement, replacing throw out bearing and flywheel as well at that time.

At 219,00, the original engine was burning approximately two quarts of oil every few weeks and was misfiring. The car was parked for about a year until I was able to source a new engine. A few weeks ago, I finished replacing the engine with a 3.5 from a Maxima that had 65,000 miles.

The car ran fine for about two weeks off/on while I was in the process of getting it inspected and chasing some power steering leaks. However, beginning last week, I began to notice a squealing sound when the car was in neutral with the clutch pedal fully released. When the pedal is pressed down even slightly, the noise goes away. This did not happen at any point before the engine replacement and did not happen even immediately after the engine replacement.
I can also slightly hear this noise at times when shifting as soon as the pedal is released for about a second, but it goes away as rpm's increase.

Here is a video of the sound: https://www.youtube.com/watch?v=PlrXfbFgm7E

Now, I have also noticed that it is occasionally difficult to shift out of gear, but I have only noticed this when downshifting. No issue shifting up, but if I am engine braking and trying to shift down from let's say fifth to fourth, the shifter becomes much harder to push out of gear. If I release the clutch pedal and push it down again, most of the time it comes out of gear just fine. If I force it when there is some resistance, I can feel like a slight "pop" in the pedal. Otherwise, the car shifts and drives just fine.

Any ideas here? I am not a transmission/clutch guy. I had help when the clutch was replaced and do not have a ton of experience with either, so I do not really know what exactly the issue would be. if the transmission needs to come back out, other than obvious signs, I am not really sure what I need to be looking for so I would like to get some ideas before getting to that point if I can.

When the engine was swapped, I did drain and refill the transmission with Redline 75w-85. I checked to make sure it was still full and there are no leaks. I am not abusive to the clutch ether the original lasted to about 200,000. I have a long drive back and forth to work everyday that is mostly highway so I take it pretty easy.

Please help!

Thanks
Justin