xACT is good
Vuze is ok, but Transmission is much simpler like uTorrent.
SHN/FLAC playback... I don't play them back in those formats - I use toast titanium to convert to apple lossless and dump into itunes.
organization is an open-ended thing.
For moving stuff, if you can get used to spring loaded folders and using column view with "shortcuts" in the "PLACES" section, drag/drop is very easy. It just takes getting used to. I use both this here and cut/copy-paste at work and can do both with equivalent speed. I must say that since I use my mac for personal stuff, I like drag/drop better.
Did you have your files in iTunes on a PC? It'd be the same on any computer. You can use automator if you want to batch-rename files. It's fairly easy but won't pull the names from a table or anything. You should be able to find something to apply tags etc around the web. If you can explain exactly how you need to rename files, I might be able to help more.
If you are concerned with organization generally, I can explain that too. Force yourself to use spotlight and you'll be able to find anything, but if the folder structure is weird to you, give it a bit of time. You'll realize how much better it is.
You can look up on the web how to fix your mouse. I actually took mine apart, but you really don't need to go that far until the other methods just don't work any more. Plus, you have to glue it back together and taking it apart is more like breaking it apart carefully. There are videos on youtube, but generally flip it over on a clean sheet of paper and roll it on the ball in a circular motion... Applying a small bit of alcohol (even vodka works) or using an air-can in conjunction with the "rubbing".
-Use a "lighter" torrent client, Transmission
-FYI, even though I also use toast titanium, you can burn right in the finder with a right click and select "new burn folder" for archival and in iTunes by creating a playlist for audio and clicking burn. Again, I still prefer toast because I'm used to it and use it for other things too.
-Column view is tits. You can drag any folder to the "PLACES" section on the left and get to it easily.
-Utilize spring loaded folders with drag/drop. You can adjust the delay in finder prefs.
-Use spotlight (cmd-space). I even use it to launch apps that I don't keep in the dock. It's really easy for that and finds stuff easily too.
-The feature that I think is the biggest win on a mac that you never hear about is quickview. For most files, you can single click on the file, then hit the spacebar and the file is displayed in a window. This works great with pics, text, and especially if you want to just hear a quick sample of a music file without opening an app - unfortunately it won't work with shn/flac but whatever.