I'm using the Apollo 4060 in my A3000, doesn't need the INT2 mod as it uses it's own mod. Sadly it patches the scsi.device in some strange way so you can't use the scsi updates from OS3.5 or 3.9. The Apollo SCSI is crap so don't bother using that.
I have the A3k in an Elbox tower so no space problems, teh Apollo 4060 won't wit in a desktop version though but there's a 3060 version with only 64 MB RAM.