> or getting a "clicking" noise across clips that I had to remove by manually fading in/out each end of the clip

Are you sure this isn't just the typical "clip/crop a sample at the wrong moment, in the middle of a soundwave, and you'll get a pop/click"? This problem happens all across DAWs and hardware samplers and such, usually there is a way to "align to zero-crossings" when you wanna avoid it, or called something similar. I'd be surprised if Audacity didn't have that optionally since before, or that they didn't have it before but now with Audacity 4 it would suddenly be used automatically, that'd be somewhat strange too.