Okay, so I've tried a few things out...

1. Fdisk /mbr – “error reading fixed disk. The master bookt code has not been updated”
2. Wipedisk and then fdisk /mbr directly after – “the master boot code has not been updated”
3. Mhdd – Reading through the documentation it looked like this wouldn’t work in a 486. After running it anyway I got the message “Need Pentium-compatible CPU”. Is there a specific version for 486 CPUs?
4. Linux commands – I’m not familiar with linux, do you have a recommended set up and is there any documentation for me to get this working in DOS? I tried to us mulinux, but I need to wait for my floppy disks to come as the gotek has a maximum of 1.39mb

not sure if it's relevant but older harddisk drives were not IDE. People just call things IDE now but maybe your harddisk controller is to blame.

It's not going to be a 1GB MFM/RLL drive, and a SCSI drive wouldn't show up in the BIOS.

Warlord wrote:

not sure if it's relevant but older harddisk drives were not IDE. People just call things IDE now but maybe your harddisk controller is to blame.

It's more the other way around. People continued to use the term "IDE", even though there was no IDE anymore when it became ATA-1 in 1990.

The term MFM/RLL isn't correct either. These are encoding schemes that were used for IDE, ESDI, and SCSI drives for years as well. MFM/RLL does not refer to an interface. The interface is ST-506 (MFM) / ST-412 (RLL).

It's a Seagate Medalist ST31082A which I think is ATA3. I'll hopefully have both the floppy discs and hard drive to usb cable no later than Wednesday which should allow me to try a few more of your suggestions. For now, no luck correcting the HDD sadly

I haven't ruled out the controller, I have another controller coming likely next week shortly so will try the HDD with that if everything else fails.

derSammler wrote:

The interface is ST-506 (MFM) / ST-412 (RLL).

Both ST-506 and the original ST-412 are MFM.
The difference is that the former is without buffered seek, and the latter with buffered seek.

In both interfaces the data is transferred in analog form, so in theory it's possible to use any of them with any data encoding - FM, MFM, RLL, ARLL, GCR...
In practice, when RLL appeared, all the drives were already with buffered seek, ie. ST-412 like.
And ARLL appeared even later.

derSammler wrote:

Warlord wrote:

not sure if it's relevant but older harddisk drives were not IDE. People just call things IDE now but maybe your harddisk controller is to blame.

It's more the other way around. People continued to use the term "IDE", even though there was no IDE anymore when it became ATA-1 in 1990.

IDE is clearly writen on the interface boards and later near the mobo hdd connectors right up to when SATA was introduced.

AJ49er wrote:

Okay, so I've tried a few things out...
4. Linux commands – I’m not familiar with linux, do you have a recommended set up and is there any documentation for me to get this working in DOS? I tried to us mulinux, but I need to wait for my floppy disks to come as the gotek has a maximum of 1.39mb

Would'nt bother with muLinux. There are one-three floppy linux tools available. If your system doesn't boot off cdroms you can use PLOP, even on a 486. Not looking good though.

What is the system specs you were trying to get the drive sorted on?

Grzyb wrote:

Both ST-506 and the original ST-412 are MFM.

The point is that RLL was introduced for the ST-412 interface. There never was an RLL-capable ST-506 controller. Of course, back then the interface was just called "Winchester", but that's a different story. 😉

Caluser2000 wrote:

IDE is clearly writen on the interface boards and later near the mobo hdd connectors right up to when SATA was introduced.

Which doesn't make it any more correct. IDE saw its end with the 504 MB limit, since IDE remained register-compatible with ST-506 and had to adhere to its limits. Also, "IDE" was not even an official term back then. Western Digital invented that, not knowing whether it should stand for "Integrated Drive Electronics" or "intelligent Drive Electronics". When it became a common standard in 1989/90, breaking old ST-506 limits, it got officially called "ATA-1".

Yes, the term "IDE" was in continuous use till the very end, but that doesn't make it right. It's just the lazyness of people to change their behaviour, and there are many other examples of that.

So I got my IDE to usb cable today and did a surface test on the HDD...just over 2000 bad sectors...I think I've found the problem