Sorry this seems to be coming a bit late, I've only just seen your question.
To allow Alt+RMB, the best option is to switch the Alt key to the Super (Windows) key using dconf-tools.
sudo apt-get install dconf-tools
Under System Tools, you should now have dconf-editor. If not, just enter:
in a terminal.
Open org -> gnome -> desktop -> wm and choose Preferences.
Look for mouse-button-modifer in the list. It will be set to , click on that to edit it and type:
Press Enter to set the value. You don't need to "save" it. Just close the editor.
That will allow you to use Alt+RMB in Blender.
Unfortunately, this will disable the Alt part of the Ctrl+Alt+0 to align the camera to the current view :-)
To fix that, change the setting in Blender:
File -> User Preferences -> Input -> 3D View -> 3D View (Global)
Towards the bottom of the list, you'll see Align Camera To View, with it's default of Ctrl Alt Numpad 0. Click on that and it will ask you for a new key combination. I use the Super (Windows) key instead of Alt for this now, so just press Ctrl + Super + Numpad 0 to set that. Note that this will show as "Ctrl Cmd Numpad 0"
For your last problem, I'm not sure why you're having issues with the subsurf shortcuts. It's never been an issue for me, so I'm not sure what to advise. You could try the Blender input settings. They're under the same User Preferences -> Input tab, but they're listed in two places. You'll probably need to update them under both 3D View -> Object Mode and 3D View -> Mesh.