M6700 Storage Issues

I ran into an issue that im curious if anyone else has seen. I have a Precision 6700 with a quadro K4000M. I left it transferring a batch of files over an sftp link overnight. When I returned the following morning, the login screen was shown mostly black but I could see the box, so I typed my password and logged in, got a flash of my desktop, then BSOD. Following this, the system would not boot. I had a destroyed MBR, and when that was repaired windows gave me driver errors immediately and crashed (BSOD with a generic error code pointing to a driver issue). My options were recovery console and remove drivers one at a time, or reformat. Since I have solid backups, I went the format route. I started having trouble getting the system to boot from a windows 7 dvd and reformat the drive and realized that the storage driver was not reliably detecting the hard drive. In some cases, the access to the drive would drop out while the system was running under load (eg installing windows or trying to create a partition and format it).

Now that I suspect hardware, I started with the usual memtest86 bootcd and system rescue cd. Memtest came back clean with no issues. Sysrescue ran fine, as did knoppix off the dvd. The drive (A samsung 850 pro ssd) is fine in another system. WLI is 1%, no unrecoverable errors, no reallocated nand yet. Clean bill of health.

When I can get the freshly installed system to boot, it seems to run fine, however when I reboot more often than not I get an error with no boot device, or in some cases it starts to boot, cuts out, and triggers the windows startup repair. When it dosnt see the drive, I power off for about 15 seconds, power back up and it boots up fine.

In order to rule out some odd compatibility issue with the samsung 850 pro (even though its been running for awhile with it) ive got a mechanical drive ill be trying out next. If that exhibits the same issues, I have my options narrowed down to a replacement motherboard, or going after a 6800.

Anyone have any other idea on what I could try before ruling it the intel storage controller on the mobo?

And lastly, if I do look to get a barebones 6800, anyone know what all I can take over ( if my k4000m will just drop in and work on it, the bluray drive can move over ect) or would I be better off sticking to my 6700 platform and just replace the board with a $250 refurb off ebay?

Edit :
Boot problems range from Invalid partition table, to a disk read error has occurred ctrl-alt-del, to just hanging on the windows logo startup and needing to power cycle. Problems seem less frequent with the mechanical drive (sata2, not sata3. 5200 rpm - much slower) but still occurring. Rebooted 5 times in a row with no issue, then a partition error, 3-finger salute, a hang at starting windows, hard power cycle, aborted startup repair, and back up. Im hesistant to spend all day tomorrow reinstalling the Autodesk product design suite through the several versions I use knowing the disk writes arnt exactly reliable.