there is a way to make the file number follow the shutter count. Here is what I did
Take a picture and find out the shutter count for the camera from it (
Check shutter count online - My Shutter Count.com)
In the camera, go to "menu" > "4" > "memory" > "2" > then uncheck "file no." at the bottom.
Rename the last 4 numbers of the image you uploaded and got the shutter count from, to the shutter count of the camera.
Put the Memory card back in and take a photo. The next photo's # should be one higher and should now go along with the shutter count.
Go back into the memory menu and check the "File No." box.
But if you delete photos during preview after taking a shot before it is saved, the file number wont increase, but the shutter count does, so this causes it go out of alignment again.