You overloaded the M2.
Here is what I think happened:
Pre-Car2PC: All good. No worries. Pushing the very upper limits of the 5v rail.
Added Car2PC: At and a little bit over the maximum draw on 5v. A laptop HD draws its power from the 5v rail. When a harddrive spins up initially either via booting or coming out of sleep, it draws the most power by spinning full speed. So on boot, with the additional USB draw, there was not enough power for the HD to spin up, so it failed boot check, and the system decided there was no boot sector so didnt boot/resume correctly.
Switched to 3.5" Drive: Got rid of the overload on the 5v rail, and moved the overload to the 12v rail. While a 2.5" drive takes all its mojo off the 5v, 3.5" drives use the 12v rail to spin the platters (which are bigger and usually much much much much much less efficient) and 5v rail to power its logic (the chips and such). So you dont have anything that would notice (like the usb not working) with an overloaded 12v rail. The CPU will go slower and things will get hotter, but not something noticeable usually unless you are looking for it.
Now: So after some time of being overloaded, the M2 does it what does best when being overloaded. It fails. Now the M2 failing may just blow itself up, or it may blow its 12v regulator and now you are passing 13.8v to a highly sensitive electronics component. So essentially you bbq'ed your CPU and maybe even your RAM.
Your M2 is most likely damaged as well. If it is still passing on voltage, then it probably is just that regulator. Check the 12v line as you vary the input voltage to the M2. Dollars to doughnuts it will output what you input with no regulation. (car is 13.8, so hence 13.8 out of the 12).
Also your mobo/cpu since they are integrated is hosed. I would check your RAM as you may need to buy more. Not just plug it in and see if it works, plug it in and run memtest86. For 512Mb on a M10k it took a little over 8 hours. For 4Gb on a Pentium 4 3.0Ghz it took roughly 5 days to check every sector.
So now you have learned a valueable lesson. Dont just assume it will work, prove it will work. Or else you will have another expensive lesson.