Ok guys, I wrote this guide a while ago and posted it to the GameSX wiki, but for those who haven't seen it, here it is.
Modifying a 6-button Genesis/MD controller to function as an X68000 6-button pad
Step 1: Open up your 6 button Genesis/MD controller and expose the printed circuit board
Step 2: Locate the small white molex connector that connects the controller cable to the board
Step 3: Cut the black (#1), grey (#7), and white (#9) wires directly in the middle, so an equal length remains on both sides. From now on the half of the wire connected to the white connector will be referred to as the “controller side” and the half of the wire connected to the cable as the “cable side”.
Step 4: Re-connect the wires in the following way: NOTE: The copper wire inside the genesis controllers is of very poor quality and breaks easily, so is it advisable to wrap each solder joint liberally with electrical tape immediately after making the join or the wire is apt to snap.
Step 5: Make sure that all your solder joints are insulated, then close the controller up.
Now, your pad will function with any game as if you are using the MD-to-X68000 adapter that came with Street Fighter or Atomic Runner Chelnov, as well as any FM Towns games requiring similar adapters. So, the mod negates your need for the adapter.