Lenovo U410 takes 10 minutes to turn on - Please help

Background:
Got the laptop - 500GB HDD and 24GB mSATA SSD with iRST/ExpressCache. iRST was by default enabled in BIOS.
Upgraded to 8.1 a few days after its release. Everything ran fine for a while.
And one day after opening up the laptop and waking it from sleep I got a message saying "It appears Intel Rapid Start Technology is not enabled on your system." Since then the laptop takes 10 minutes to start where as before when I got the new machine it took 20 seconds.
I did a system recovery using OneKey but that apparently only restores the C:\ drive so the mSATA (D is still having issues that are causing the long boot time.
I tried a few things like deleting the mSATA volume/recreating and that did not help. iRST since the error message in the BIOS is showing as INVALID. I can't use diskpart to clean because the mSATA does not show when doing a list disk. I've changed AHCI to RAID and I can't get Windows to launch or go into the troubleshooting command prompt because Windows has an error when trying to start up and it will just boot loop.
At the moment if I power my machine on from a powered down state it will start on a black screen that will sit there for 5-8 minutes and then the Lenovo screen with the loading circle will take another 2-3 and finally when Windows launches the system will be slow for another 2-3 minutes before I can even open the Task Manager. If I try to restart when Windows is loadaed it will just stay at a black screen until I hard-shut down using the Power button.
I really don't know what I can do without voiding warranty (I thought about taking the mSATA SSD out but don't want to void the warranty). I really don't know what could have caused this (maybe upgrading to Win8.1?) but it's been happening since I woke the computer up from sleep once. I've heard that Lenovo Energy Management might be a cause of the iRST issue too?
I'd also like to note that I tried uninstalling iRST and the uninstall was OK. Upon trying to reinstall it iRST is saying that my system does not meet the requirements which obviously is incorrect.
Can someone or support please provide some help? Is there a way I can image my system (both HDD and SSD) to factory?
Thank you.

I've also tried reinstalling ExpressCache but to no avail - it says during the install a suitable drive was not found.
Doing a eccmd.exe -info says a SSD is not mounted.

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