Starting Windows taking too long; can’t access hdd, disk mgmt

Pls help! I use my computer as my media server among other things and I usually keep it on for almost 1 week and I routinely shut it down for a few hours or more then turn it back on. The last time I did, I remember it asked me if I wanted to force shut it and I did. So when I got back to turning it on after 6 hours or so, it took a long time when it got to the starting windows screen (black screen with windows logo). So I restarted it, but it still took a long a time when it got to the said screen. After I logged in, I realized that I cannot access my second internal hdd (I have 3 x 2TB, one is installed with windows 7, the other 2 WD Red NAS HDD are dedicated to media files), but I can access my 3rd internal hdd just fine. Other than that, in the navigation pane in explorer, the name changed from "Media Server (E:)" to "Local Disk (E:)". Also I noticed that it displays 2 cd-rom drives when I only have 1 dvd rw. So I checked disk management and it doesn't load up. It says at the bottom of the window:"Connecting to Virtual Disk Service". When I shut down my computer, it also took a lot of time. Also when I tried going to safe mode it still took a lot of time.

I googled and I've tried the following:
1. Booted, pressed F8, selected "Repair Your Computer," but I didn't proceed because it still took too long. So, i rebooted.
2. Scanned for viruses, none found
3. Scanned for malware but never finished "checking for updates." Took more than 1 hr. I cancelled.
4. Tried sfc /scannow in cmd... "found no integrity violations"
5. Tried DISM /Online /Cleanup-Image /RestoreHealth in cmd... showed "Error: 87 The restorehealth option is not recognized in this context"
6. Created new user account, but loading was still slow. Same issue with hdd.
7. Hardware and Devices Troubleshooter in control panel. I'm forgetting the results but I think it only reported my bluetooth. Tried it again but won't load anymore.
8. Fixing disk management from services window. Nothing.
9. System Restore. Did not complete successfully. It reported that it could not access file due to Anti-virus running. I didn't try again without anti-virus since the procedure took about 48 mins to complete.

Other symptoms:
1. Rainmeter skins on my desktop behaving weirdly. Network skin DL: 14.6 MB UL: 5.8MB, when my subscription is upto 375+ KB DL (or 3 mbps) only. Clock skin freezes then catches up after 5 mins.
2. When opening some apps sometimes it takes too long to respond. Particularly, malwarebytes.

Pls help! Thanks.

The fact you did a force shut down has likley corrupted the disk it will take some time but do a full disk check with chkdsk e: /r then change drive letter and test other drives

You may also want to check out the SMART data. It's not always indicative of HDD issues, but it's worth a shoot. Use Crystaldiskinfo or HDTune. There is also HDD Sentinel.

There's also a boat load of tools here. I've used HDD Guardian in the past.

@SIW2... My system would not boot to winre, but I was able to use system restore from safe mode. I felt that my system ran a little faster, but other than that nothing's changed.

@samuria... I'm currently running chkdsk and I'm already at stage 4 of 5 (chkdsk is verifying file data). It's been more than 12 hrs now, but i still am gonna wait it out. Also, i was able to finally load disk management (took some time to load), and it says that drive e:/ was RAW and not NTFS. Should i be worried?

@F22simpilot... sounds like i need to do this too. I'm gonna try your advice next.

Michkelo said:

Also, i was able to finally load disk management (took some time to load), and it says that drive e:/ was RAW and not NTFS. Should i be worried?

Sounds like a hard drive issue.

It's almost 2 days now since i started chkdsk and it's still in stage 4 of 5 (chkdsk is verifying file data). Should i just quit it? or wait for it? It's weird that disk management is saying that e:/ is RAW while chkdsk is saying that it's still NTFS and it's got the volume label correct -Media Server, unlike explorer and diskmgmt saying it's Local Disk. I read somewhere that getting changed to RAW from NTFS might arise from a malware, but i scanned using malwarebytes and it didn't get anything. So if it's indeed a hard drive issue, what should i do? And why is starting windows taking too much time when the supposed culprit is e:/ when windows is installed in c:/?