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So for the benefit of anyone who may come across this later, there's 2 solutions to this problem that have worked for me as suggested by the other posters here:

1. Put the standard or Hybrid HDD into an external enclosure and boot to it over USB3. It works and it's cheap, but it's not elegant.

2. Put in an SSD - There's something up with the Logic board (probably the SATA controller as explained in previous posts). It works with an SSD at full speed apparently flawlessly, but it doesn't like HDD's or Hybrid drives, even if they're OEM. Probably a design flaw.

Details:
I started with an HDD and moved to a Hybrid SSHD that would intermittently slow down to 11 MB/s per Black Magic Disk Speed Test.
After success with an external HDD (as suggested in this thread) I knew the computer wasn't totally borked so I bought a Samsung Evo 850 (not pro) that I knew I could just use in another project if it didn't work in the Mini. I cloned my working HDD to the new SSD and then put it in the external enclosure first, and got like 380 MB/s consistently (after repairing permissions, that part was making things funky, but a permissions repair got it working right).
After that external SSD over USB success, I put the SSD in the Mini where it's supposed to go in the standard slot, and now I've had 480 MB/s read/write for the last 3 days. That's over a 43x increase in speed and usability compared to the 11 MB/s I was getting. There've been no slow downs or beachballs or any of the old behavior. Thanks to the posters who helped, and good luck to anyone else who comes across this problem.
 
Good deal.

Most Macs play nice with most drives...but there have been exceptions. Usually SATA controller, but not always. Looks like you found an incompatible drive.

Glad it got sorted, and you wrapped it up.
 
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Hi Elliots11, thank you for this solution. I've been trying to solve the same problem for quite a while now. Can't wait to have the spare time to try it.

Just a clarification:

Method 1, did you leave the internal HDD empty? If so, did you have to tell the mac where to boot from, or does it find it automatically?

Method 2, did you have to clone original HDD onto the SDD? Or can you install a bootable version of OSX onto the SSD right out of the box?
 
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Hi Elliots11, thank you for this solution. I've been trying to solve the same problem for quite a while now. Can't wait to have the spare time to try it.

Just a clarification:

Method 1, did you leave the internal HDD empty? If so, did you have to tell the mac where to boot from, or does it find it automatically?

Method 2, did you have to clone original HDD onto the SDD? Or can you install a bootable version of OSX onto the SSD right out of the box?

Hi, sorry for the slow reply, only on here periodically.

Method 1 - yes I left the internal drive bay empty. You can specify which disk to boot from, including an external USB drive, by holding option when you boot up and hear the startup chime. A screen with all the attached HDD's that are bootable will show up and you can pick the one you want to boot from. I don't know if it'll boot to an external if it were the only available boot drive and you hadn't told it to boot from there previously, I would think it would so long as it sees a boot drive available, test and see.

Method 2 - You can create an install USB thumb drive and use that to setup your machine, so no you don't have to create a clone of your boot drive. Macs also have internet setup when you press the D key on boot, but I don't know how well that's going to work with just a blank hard drive in there, OS X creates an install partition and that's what's used.
 
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Hi, sorry for the slow reply, only on here periodically.

Method 1 - yes I left the internal drive bay empty. You can specify which disk to boot from, including an external USB drive, by holding option when you boot up and hear the startup chime. A screen with all the attached HDD's that are bootable will show up and you can pick the one you want to boot from. I don't know if it'll boot to an external if it were the only available boot drive and you hadn't told it to boot from there previously, I would think it would so long as it sees a boot drive available, test and see.

Method 2 - You can create an install USB thumb drive and use that to setup your machine, so no you don't have to create a clone of your boot drive. Macs also have internet setup when you press the D key on boot, but I don't know how well that's going to work with just a blank hard drive in there, OS X creates an install partition and that's what's used.

Thank you very much. I will give this a try as soon as I gather the necessary items. Some things aren't easy to come by in the current country I'm in, and by that, things can get pricey. I hope one of these methods works for me. Otherwise, I'm stuck with a fairly expensive paperweight. Thanks again. =)
 
Hi Elliots11, thank you for this solution. I've been trying to solve the same problem for quite a while now. Can't wait to have the spare time to try it.

Just a clarification:

Method 1, did you leave the internal HDD empty? If so, did you have to tell the mac where to boot from, or does it find it automatically?

Method 2, did you have to clone original HDD onto the SDD? Or can you install a bootable version of OSX onto the SSD right out of the box?

1. You can hold down the Option key on any Mac to see all of the bootable Oses available. For many machines it would only show one, but it will show: USB, TB, FW on older Macs, Optical drives, and network drives.

2. You can do either, clone or install a new OS...or a bootable installer. Just be sure to format the new HD or SSD HFS+ first (or APFS for the 10.13 on an SSD).
 
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