Agree with Britton30, the SSD is mSATA and the HDD is SATA connection, they can't be swapped, different connections.
Need to see the Disk Management snip and if it is MBR or GPT.
will auto install from Windows, they probably went to the HDD OS.
In your post #28 you have 'Intel Smart Response Technology' enabled, this may need to be disabled, leave it unless you are having more problems. Intel® Smart Response Technology User Guide The Definitive Guide to Clean Install OS on a mSSD Cache Equipped Laptop
Found this quote in the above link, post #19:
Also the master boot record has to be on the sata0 disc drive. I also followed the definitive guide also you can not delete the other os untill you set up a mbr.
Note: I would not use a large SSD (40GB or larger) as a cache system (Intel Smart Response Tech), installing the OS on the mSATA SSD will have much better performance.
I had a similar issue when I installed Windows 7 and Windows 8 UEFI/GPT on a new SSD, had Windows 7 installed on my HDD and couldn't boot until I secure erased the HDD, formatting the System Reserved and OS partitions didn't help, it must have been the MFT (Master File Table) on the HDD. Another HDD that had no OS installed did not affect the boot process. When the problem HDD was erased and added to the system, it would boot normally.
This is probably causing your long boot and shutdown times, the BIOS and OS are searching the HDD for OS installations. Wipe/clean the HDD, if you don't have anything on there that you want to keep.