Sam,
Do you have any pictures from your engine project that shows how you mounted the battery when you cut the tray? I will finally pick up the engine next late next week and start the rebuild process. Here are some pictures of the beast stripped down. Plus some of the wiring changes. I had to add a diode to the starter to provide power the the EFI circuit while the starter is engaged. Plus a diode on the PTO so the coil does not shoot voltage back down the positive line when the field collapses. Finally I added a diode to the positive side of instrument light number one. This was done on later cyclops cubs, so I decided to do it as long as I had it apart. I took the main voltage supply line from the left side and moved it to the right where it will attach on the new motor. I did this for the oil pressure sensor and magneto kill line as well. Just for fun I replaced the instrument and tail light bulbs with LED's. I have the new brake pads installed, they are 1/4 of an inch.
Diode starter.JPG
PTO Diode.JPG
Wiring Center.JPG
Brakes.JPG