Welcome to Tom's Hardware, @Olosen113!
It sounds like there could be some sort of an OS confusion, whenever you connect the secondary 500 GB HDD especially if it contains an OS installation from a previous system. What happens when you boot into your primary WD HDD without having the secondary drive connected? Is the issue still present?
If it's only happening when connecting the secondary drive, I'd advise you try using an external enclosure (with an AC adapter) or a docking station to connect that particular HDD externally without it interfering with your system's boot. Once you have it successfully connected to the PC, you should be able to see it in
Disk management in Windows. From where you should be able to
reformat it and wipe the HDD clean in order to get rid of the old files.
Another alternative would be to plug it in the system and try booting into the
Advanced StartUp Repair Options from your Windows 7 installation media. It would allow you to fix the MBR (Master Boot record) and hopefully get rid of the 'Bootmgr is missing' error.
Hope this helps you. Let me know how it goes.
SuperSoph_WD