Primary Master Hard Disk Error

Not sure if the answer to this is spray a little WD40 into the carburettors.

When I boot the PC from cold in the morning I get "Primary Master Hard Disk Error" during boot up. The strange thing is that after 20 mins or so of reboots or leaving the PC switched on at the boot up screen it will restart fine. I can't see any issues with the BIOS and the PC hardware is unchanged in the last 5 years. This issue has been consistent now for 4 months. Once working there are no noticeable issues with the PC.

Any thoughts on what needs to warm/charge up before I replace the HDD and discover the problem has not gone away?

Assuming you have tried different cables I would backup and change the hdd asap.

does the hdd make clicking noises? or try a different cable or check psu voltage

Almost as soon as I posted this, the drive started making a lot of mechanical noise. I backed up onto a second disk and replaced with an 128GB SSD.

Primary Master is indicative to using a PATA interface for your drive. With that information alone, I can tell you that your drive's getting old. You need to copy everything to a new drive and look at replacing your old system sometime in the near future.
If your system isn't old, then you should probably check the SATA settings to make sure that you have AHCI enabled instead of IDE. If so, you have a weird system to be indicating Primary Master has failed. If it's not enabled, you'll have to reinstall your OS to take advantage of the significant gains it offers.
Also, see the post about S.M.A.R.T. monitoring. A linux (Ubuntu or Fedora) boot CD/DVD could help you to determine if the drive is about to fail by reading the S.M.A.R.T. data and giving you a more detailed look at what's going on with your drive. Alternatively, you could try making a boot disk of MHDD and using its S.M.A.R.T. test feature.