@SinclairSpeccy After been reading through the paper from 2020 on the boot sectors in use by the #ElkCloner, it is clear that to get it working, the disk should be a slave and not a master disk. There are three areas of the boot that needs to be adjusted, track 0, track 1 and track 2. On track 0, the area $0A00 ... $0B00 should contain the loader part of the Elk Cloner. On track 1, the jump located at $1080 should be modified to jump to the Elk Cloner code instead of the regular DOS part. On track 2 the Elk Loader should be installed from $2300 ... $2400 (it occupies only two sectors and even though there is more empty space after the occupied part, it overwrites a few bytes at the beginning of $2300 which are set, but obviously not used, $00 and $ff bytes). I have been sitting looking with hexedit on original disk images from DOS 3.3 analyzing the structure and what happens to it with different alterations using image tools. The AppleCommander seems to refuse to overwrite the boot sector of the image it creates, so it is not that straight forward to get it on e.g. location $2300 with e.g. the small utility 'ac' from the #AppleCommander package.

@SinclairSpeccy The binary file should probably not need a separate linking stage since the #assembler #Merlin32 is capable of dealing with the 'org' defs in the source file (multiple segment source file with absolute segments) as is and the two fixed segments in the source code sets them to 9000h and 9500h, latter labelled 'loader'. There is probably a bunch of tricks to this boot sector #virus. I installed the #linapple #emulator on my #debian 11 #linux workstation and then used the #AppleCommander to create #AppleDOS disk image onto which I placed the binary. I toyed around a bit with placing the binary at some various sectors prior of loading the 'dsk' file into the emulator. I then tried with using the 'INIT' command setting the virus binary as the executable and rebooted with it, though I cannot report that it works as is. There is more to it IMO regarding required sector locations. See e.g. this archiv.org paper for more details: https://arxiv.org/pdf/2007.15759.pdf
As you can see, it is expected to be located in one of the reserved sectors for relocators, so it must be on a master boot disk (not a slave disk) with relocator (the virus wants to sit in a relocator sector) and the boot must init the virus (maybe possible by just setting it with INIT)
Kind of ran out of time on this experiment. If I get moving on this again, I will let you know.