Ryan
Yes you can delete the ncf files, STEAM will automatically update any missing DLC purchased.
I recently deleted The Portland Terminal by mistake - I just removed the ncf file and the DLC was replaced on my next steam session.
Stopping some processes is not the same as a clean boot. Clean boot virtually stops them all and is a way of determining if something in Windows is stopping the app from working, but its unlikely in this case. Have you tried running RW in "SAFE" mode?
Have you tried defragging the drive railworks is on and using windows disk cleanup utility to remove any rubbish. (or CC cleaner if you know what you are doing)
Is it worth running sfc/scannow to see if their are any corrupt system files?
Yes you are correct about WMC - however SP3 plus any later updates did change a few things. I was confused by the SP2!!
But its a mystery why some scenarios run OK and not others!
Regards
PeterH