The latest version is now 3.043.062, patched to work with Windows 10
3.043.066 was removed, because it no longer worked in Windows 10.
Yes, you basically just install the new version, and copy the backup files over the existing ones.
The .xml file you want is in the main Mach3 folder, with the same name as your profile.
If you want to get back to your current setup, just copy the entire Mach3 folder, and paste it over the current one.