Item # 1 may be as simple as updating your FRUSDR so that it would provide the correct sensor data records for the fans that are installed on the system. The firmware updates can be found here.
Item#2, on the TPS, there is a good read on how to populate memory on the server board on section 18.104.22.168 (page 21) as well as requirements for memory use. Also, check if it against the tested list available here.
Item#3, depending on how you configured your storage device, you may need to install additional drivers.
Best of luck.
Items 2 & 3 was solved, still strugling with fan speed and amber light though.
Did you try updating the firmware as suggested earlier ? If yes, can you check the SEL for possible errors. Depending on what you want to use (& the OS you are running), you can try the Intel® System Information Retrieval Utility for Windows* or System Event Log Viewer for UEFI, Windows and Linux to generate the SEL.
I did do firmware update as per you original post.
On closer inspection I found that the hdd fan was plugged into fan 3 instead of fan 2, all problems now sorted, thanks for your help!