Hi Welcome to DUC. Lots of info there, but the most important stuff is unfortunately missing.
What is your audio interface/Playback Engine set to?
What HW Buffer size are you running at? That is the primary tool to help mitigate CPU errors... increase it and see if the errors decrease
And then what sample rate are you running at? Just work at 44.1 or 48kHz for now.
But, and this has been covered in literally hundreds of threads on DUC,... if you are running ASIO4ALL or WASAPI just give up. If you want to run any Pro Tools products you should have an ASIO compatible interface with an ASIO driver supplied by the interface vendor. I don't care what others might get running, or that Avid says other stuff might work. You need to set stuff up so you have an expectation that it *will* work reliably under load, and with Pro Tools on Windows PCs that's means you need an ASIO interface.
And did you optimize the computer? (see instructions under "Help us Help You" up the top of each DUC web page).
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The usual several restarts.
Checked my drivers are up to date
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Drivers for what? The only one likely to matter is the ASIO interface which you are apparently not using. Very rarely GPU drivers might matter.
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Done a defrag
I tried bouncing the tracks down to a mix and just playing the mix and it's still the same.
I tried copying the mixdown to my C drive and just playing it through audio player and it still cuts out like the mix itself has been recorded with the cutouts in it.
I haven't yet tried a different track as the other tracks were recorded in Cakewalk so I need to import them yet. But I will try that over the weekend.
I deleted almost all unnecessary software on my PC to keep it as clean and free as poss.
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I love all the great detail in your email, but unfortunately nearly all that you tried is likely a waste of time. You should start with the standard troubleshooting steps under "help us help you" up the top of each DUC web page. Always start troubleshooting by trashing prefs. Which you have not done? And then after trying with an ASIO interface and larger H/W Buffer size if needed. If you still have problems you should be looking at plugins (*always* suspect plugins with CPU errrors), starting with removing all .aaxplugin files from the plugin folder and seeing if Pro Tools runs reliably after that. All standard stuff to try before even posting here. And if you have Cakewalk installed and have installed third party plugins for it I'll bet good money they have also dropped AAX plugins into Pro Tools.
As you troubleshoot make sure "ignore errors" is not checked, you want even minor errors to cause a failure.
Nothing here is likely due to the drive, but in general get rid of the HDD, no reason to be using a HDD in this day and age, or SATA... I suspect your motherboard has M.2 PCIe 3 slots, so you should be using M.2 drives in those and running Windows, sessions, samples all from that one M.2 drive (or multiple M.2 drives if you need the space). That will make everything seem faster on that PC.