First I would try just installing Mach over the top of itself.
The files you want to save are your xml, any custom macros any custom screensets and associated bitmaps and of course you licence which is called Mach1Lic.dat and is in the main Mach3 folder. Also tooltable and offsets are stored in the macro folder of the profile you use so best just saving the whole macro folder.
Installing Mach over itself should not need replacing any files but always best to have them backed up just in case
Hood