I'd definitely install Mackie OS 5.1 with the new crack, where you only need to replace a single file and have all the plug-ins authorized, already, rather than try to get V3 back on there. But sounds like you want to do that for some reason.
What happened when you were done installing the third floppy disk? Did it give some sort of message that the installation is complete, and then you rebooted? Basically what I'm asking is "are you sure the installation was complete?"
Did you take the 3rd floppy disk out of the drive when rebooting after installation? If not, it will try to boot from the 3rd floppy disk which isn't bootable, and give you that kind of error (something like "Boot Fail Floppy Disk" or similar).
So, that would be the simplest possible problem... if the 3rd floppy is still in the drive, you'll get that kind of error and it won't boot past that point
The harddrive you installed the Mackie OS on is recognized in the BIOS, I assume?
What if you turn the floppy drive off in the BIOS completely? It's not needed to boot up the mixer. For that, in "Standard CMOS Setup", where it lists the 1.44 floppy, just set it to "none".
Under "Advanced CMOS Setup", you can also change the first boot device to the harddisk instead of the floppy. Then it just shouldn't check for that on boot (unless it doesn't find the harddrive).
There's also a setting for "Floppy Drive Seek" you can turn off. This will stop the computer from doing this short "BRRRRRRB" sound, when booting the computer the first time.
Anyway... this is just to troubleshoot what's going on, and get you past the floppy fail message. Of course, you'd want to have it working, eventually, to be able to copy files, etc., but if you'd do that via FTP (or if you happen to use an SD card that you can remove via a slot on the back instead of a harddrive), then you wouldn't have a need for a floppy at all, other than installation (...and personally, I'd rather install a V5.1 clone, than dealing with Floppy disks).
I'm pretty sure this one's fixable. It's probably just a little thing you missed somewhere... I don't think it's time to worry, yet
Anyway... good luck with the suggestions above. Curious to hear if that helped.