Try a thorough HDD scan (and repair) using HDAT2, HDD Regenerator or any other similar tool out there (if any). There may be bad sectors in critical system files that just break hardware detection and/or other important functions of the OS.
Using MSConfig or any other similar tool (I use CodeStuff Starter), check if there's any unknown/suspect file(s) running at boot time. Disable everything that doesn't look critical for a normal operation (post the list of applications and services here, when in doubt). There could be either malware or a bad driver messing with your system.
If you can borrow a small test HDD from someone, disconnect your current HDD, connect the new one, perform a OS install from scratch with all other hardware connected
and if detection works OK and you get everything in Device Manager (you may install required drivers if you want, to make sure), then you can rule out a hardware failure (except maybe for your original HDD that you have previously removed). On the other hand, if you can take your original HDD to another machine (careful not to boot from it!), then you may use that system's tools to check drive integrity and any possible software intrusions.
I believe everything else has been covered in the previous posts. Good luck!
Random browsing through the 9x section brought me to a topic that just might be of help here: ifsmgr.vxd and zero-byte .inf files
This post has been edited by Drugwash: 27 December 2012 - 01:04 AM