Although I have not done a 720 to 1.44 upgrade in a Mega STE I assume that because it came with a 720 the controller is still only capable of a 720. If so then you need to upgrade the controller to run at 16Mhz and not 8Mzh, to do this you need to bypass the controller chip (I think it is a part of the Yamaha Sound Chip for some bizarre reason) and place a new crystal in its place.
As mentioned by someone else you will also need the program too (I think it changes the seek rate), you will be able to read directories and 720 disks I think.
I do know the parts and layout somewhere but before I find it you may swell check my STE - Mega STE theory.
