Just a couple of things to mention.
Since the game uses SRAM (save feature), you might want to inject it into Sonic 3 or Phantasy Star II that has it.
Rather than using the 04.app I modified, there is a much simple way of disabling the Electronics Manual without modifying the 04.app. Simple open 00000001.app in a hex editor, search for HomeButton3. You should get one result. Simple replace this with HomeButton2 and save.
The save banner image has green and blue pictures in the corner. You need to go into the "save icons" folder (where the VC_Icon_Gen.exe is located) and replace the image with a better one. In fact, I'll upload the tool with the fixed Genesis image.