At this point, I don't think the problem is with the boot files. My guess is the problem is either with a pagefile or a hibernation file being directed to the hard drive instead of the SSD.
I would look at steps 11, 15 and 16 here:
Optimize Performance of Windows 10 - Windows 10 Forums
You want to try disabling hibernation. Enable write caching for the HDD. Step 16 doesn't give you any methods, but you want the only pagefile to be active on the SSD, no pagefile on the HDD. I'm not at my home computer, so can't post screenshots of how to do that. Google would probably help more. You basically want a Windows managed pagefile on the SSD (C:\ drive) only and nowhere else.
I guess the only way to know is to open up my laptop again, remove the HDD, verify the shut down problem still exists, turn off fast startup and then try shutting down again. I will also make sure write caching is enabled. Just to be clear, on the write caching, enable it on the conventional hard drive (D) not the SSD (C) or do I want it enabled on both?
I will look up disabling hibernation through command line.
One other question, since I know so little about partitions and formatting, in my screenshot from Mini Tools I see that the system partition, that I copied to Disk 0 is formatted as Fat32 and the existing C partition is formatted as NTFS, also the system partition is listed a "Primary" instead of "Active". These are not problems are they?
On both UEFI and legacy BIOS computers, the partition the computer boots from will be marked as the "System" partition inside the parenthesis in built-in Windows disk management (your post #10). For both UEFI and BIOS computers, this partition must be a primary partition, not a logical partition, and primary v. logical is shown in the graphical part of built-in Windows disk management.
On UEFI systems - this (system) partition that the computer boots from must be FAT32 and is normally an EFI System type partition. You can have multiple EFI System type partitions and you select which one you actually boot from in the UEFI firmware settings/boot menu. There is no requirement to have any partition marked as "active" on a UEFI system because the firmware looks for those EFI System partitions.
On BIOS systems, the BIOS looks for partitions marked as "active". You can only have one "active" partition per physical disk. The "active" partition can be it's own separate partition - or the partition containing the operating system can be marked as "active". This "active" partition can be FAT32 or NTFS, but it does have to be a primary partition and not a logical partition. Instead of building the BIOS boot menu from EFI System partitions, BIOS will build the boot menu from all the partitions it finds that are marked "active". The BIOS and UEFI boot menus I am talking about are those that are accessed by pressing a function key or DEL or ESC when the computer is first turned on before any OS files load.
A big tip of the hat to you @NavyLCDR for not only helping me get my computer configured properly but for quite an education! I followed through with your final suggestions and my laptop now boots and shuts down without the D drive attached. I feel confident that I can now format the D drive for data storage and my computer will work just fine. Thank you so very much!
One final question should I turn off file indexing for the SSD drive and leave it on for the standard HDD?
Leave file indexing on. It will make your searches complete faster, even on an SSD. Glad it worked for you!