Welcome aboard! Nice ride
I just bought a used EXB myself in December so, we were/are sitting in the same boat. For rust removal, you can use electrolysis to plate the metal, but that's a bit more involved. Just grab a wire brush and after you've given them a scrubbing, coat them with a little WD40.
Are you sure the clicking is coming from the center diff? A lot of the strain is on the front diff. You can test this by lifting the rear of the car and moving the car back and forth. If you hear some clicking when you change directions, chances are that the diff input pinion is worn down/stripped and needs to be replaced (that was my experience anyways, YMMV). I suspect you'll need to replace the front and/or rear diff input pinions and then you'll want to spend a lot of time shimming the front and rear diffs properly. You really want to get them as tight as you possibly can. It took me a good while until I had the front diff tight enough so as to remove all clicking.
One other thing you should look at is the servo saver. As it comes from the factory, it's
really loose and you'll find that the front wheels barely turn when the vehicle is standing still. They'll turn as long as the car is moving forward, but there's a cheap and easy fix. First you'll want to take the servo saver apart. If you've never taken an Arrma servo saver apart, it can be a bit of a chore and if you just try to crank it open, you'll probably tear the threads off one of the halves. This is the technique I use to take them apart.
I then cut 5 shims from a card blank (bank card thickness) by drilling a couple of 12mm holes with a stepped drill (spiral drill are impossible in thin plastic) and then cutting around the hole with a pair of scissors to create shims.
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I then stacked five of these shims on top or under the one metal shim that you'll find at the bottom of the servo saver.
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Hope this helps