I just completed a mod using the OP's photos and description as a guide. Yes, the shorter standoffs that come with G5 case are the ones to use. I removed them all with a slight twist using a pair of pliers. Then lay them out and you can see which ones are the shorter ones easier. The tricky part is lining up your motherboard with the standoffs in the correct position for the PCI card slots. I put the standoffs in the holes, screwed them in and then lined up the motherboard by drawing some lines around it. Then I put a small piece of modeling clay on the bottom of the standoffs and placed it back again, lined it up and let the modeling clay stick to the case. I used these as my guides to roughen up the case and set the epoxy in the correct position. The OP used an old mATX board but I didn't have one. I have not yet checked to see if a video card fits well, all I had was the old G5 card to use a guide. I am not planning to use a video card yet so if I stay with my current setup then all is fine.
As for the minimal cuts, I only cut the backplate out for the mATX ports. I used the original G5 fan holder and replaced the fans with Noctua Redux NF-B9 fans. I also used a low profile Noctua NH-L12S CPU cooler. I used the original PSU power cable connector and soldered it like in the photo. I also bought the BCH G5 front panel cable assembly but I still can't figure out why the power LED only lights when the button is pressed and then goes out when released. I am 100% positive it is on the correct pin for the Gigabyte motherboard (PLED +) and I know the LED works because my G5 was in perfect working condition before I stripped it.