From the details you've given, it's definitely a corrupted HDD or a dying HDD. As the SSD is the boot drive and the HDD is not. So, this should not slow down either the SSD or the boot time. My advice to get back your boot time and still use the HDD is to go to the bios setup during booting and go to the boot option and remove the HDD from booting preferences. This disables searching for the HDD for boot files and makes your SSD the first priority. This might solve your Boot time problem. For the stuttering, I advice you to clean up your HDD by using some software and check for HDD failure and try repairing it. Or just buy a new HDD from BestBuy. I'll give the links for some HDDs.
Link for some HDD models: https://www.bestbuy.com/site/seagate-barracuda-2tb-internal-sata-hard-drive-for-desktops/6344172.p?skuId=6344172