I can suggest only one thing, and it is drastic and may NOT help.
What you describe sounds like an HDD that is generating lots of errors causing multiple re-reads that somehow manage to succeed sometimes. That could be a result of a bad connection, OR it could really be lots of errors on an HDD that is failing. So try this first because it is non-destructive: Shut down. Go inside and disconnect carefully both the power supply cable and the data cable to that HDD. Re-connect each. Repeat several times. Now go to the other end of the data cable where it plugs into a mobo SATA port and do the same. When done, re-inspect everything to ensure you did not dislodge something else by mistake, then close up and power on. SOMETIMES the contacts at connectors can become oxidized from the air, and this action MAY "scrub" those clean so you get good connections again. So IF your system seems "cured" you may have fixed that.
At that point I really would advise you download the Seagate free HDD utility pack SeaTools and tun its tests. The first thing it will do is report to you any clear errors messages that exist already. Then run the Short and Long tests. These are non-destructive tests (the Long one tests everything on the HDD). If either reports errors, note them down. Then you may want to consult Tech Support at Seagate for their advice.
This further step IS drastic and you can NOT go back from it. It means completely wiping EVERYTHING from that HDD so it is like brand new (almost) and you must re-Install your OS and all software, then re-establish onto it (from a backup you have??) ALL your user files. It means doing all the work of replacing that unit with a brand new HDD, but without actually buying a new one. AND, of course, if it does not solve your problem it was a waste of time. Now, I see that you already have replaced the HDD, so doing this is not quite so hard for you. If you try what I suggest next, the hope is that the old HDD's problems were not severe and can be overcome by simply "cleaning" it completely, so you can re-use it for data storage.
This step is called a Zero Fill, which CAN be done through SeaTools, but it will be preceded by a strong warning that this will destroy ALL data on the drive, and do you really want to do that? I REALLY suggest that, if you have ANY other storage devices on your machine, you DISconnect them all so that the work can ONLY affect the faulty HDD even if you make a mistake. So having done that and if you decide to proceed, go ahead. This process with go through EVERY Sector of the HDD and simply write all zero's to it, destroying all previous info. So no old junk can survive. As an important second feature, it will trigger a normal background process on any modern drive. It TESTS all writes to ensure they worked. If ANY Sector fails this, it is marked never use again and replaced from a stock of empty "spare" Sectors the HDD has had since manufacturing. Now, there is a limit to how may spares are available for this replacement, and if too many are used you'll get a warning that this may fail completely if it continues. But if the process can complete and still have a good reserve of spares, you end up with an HDD that is completely empty and with NO "Bad Sectors" to cause errors. It's just like a new HDD, but with a smaller reserve of spare Good Sectors, and some wear history.
So, IF that works, you can start again with that HDD as if it were a brand new empty HDD. You could Partition and Format that unit for use as a data drive that is NOT a Boot Drive. If not - if there were real major problems with the HDD so this cannot be done cleanly - you scrap it.