I am unsure what the issue is, but it does sound like a wear issue
The 2nd paragraph, where you mention that you coast up to lights in neutral, do you mean from speed? As in you could be doing 40mph, clutch in, into neutral, clutch out, and at 3-4 mph then clutch in and changing to 1st? If so, this could be causing some transmission wear, the output shaft (wheels) are turning but I believe that the lubrication only occurs if the input shaft is also turning, which if you are in neutral it won't be.
I'm unsure how much wear it actually causes, it might be insignificant and your issues unrelated, there was a long hill I used to coast down in neutral until I realised it was unnecessary and I caused no damage that I can tell but my gearbox is also not so many miles so maybe it will show up soon. The gears in my car are difficult to get into sometimes, but not to the same degree as yours and they don't pop out
It could possibly be the throw bearings? it would explain some rotating sounds and some howling sounds, which would point to a clutch issue, if it's happening in all gears or if it's particularly hard to change gear while you are accelerating that is something I would look at
