If you are talking about the sump are of the lower unload tube...it kinda sucks to replace. Don't know if i did it the easiest way, but you have to take the drive gear box out, the horizontal augers out, and the ratchet for the concaves has to come off. Probably would make it easier to put the combine on blocks and take that tire off too, but we didn't want to do that so we faught it in. Its pretty much a 2 day job, and a 2nd person really helps too.
On the noise you are hearing when you engage the seperator.
I had the same thing happen on our first job down south and the hired man described the same noise.
Check the strips on the rotor behind the bars, the bolts had come out of that machine and the thing was hanging and scraping on the cage by one bolt. Took just a couple of minutes to fix, but forever to find the problem. Maybe this helps, I hope it's something simple like this.