This could be quite long as I'm trying to give all details that could possibly be needed. Please read it though, I could really do with some help, I'm at my wits end!
A few weeks ago when I had windows 7 ultimate, I came across a "BOOTMGR is missing" error. This was just after cloning my old failing WD HDD (lets call it HDD2) onto a old, but perfect condition Maxtor HDD (lets call it HDD1) (not very old. Still sata). So for some reason it looked like the cloning software (EASEUS I think) for some reason hadn't cloned BOOTMGR or any boot files. Eventually I ended up sticking in HDD2 for some reason, and suddenly it worked. So I think it must of had HDD2 down as the boot drive. I assumed it was using the boot procedures in HDD2 to get into the OS on HDD1, most likely incorrect as the thing I understand least about computers is boot procedures. Always been a problem area for me. Most likely due to my stupid laziness, I never thought to fix it cause it was doing the job for me. Two days ago I 'upgraded' to windows 8 pro x64 and that all went fine, apart from a few partitioning errors (definitely not related to this). Today I got a new Seagate HDD and I was going to clone HDD1 to that and upgrade to it. I got my cloning software disc at the ready, took out HDD2 (forgetting about my little BOOTMGR setup) and stuck in the brand new Seagate. Then I tried to boot and obviously got the BOOTMGR error again. So put HDD2 back in and booted up, naturally it worked again. I researched this a bit (ubuntu - How do I move the Windows 7 Boot Files (bootmgr, ...) to a different drive? - Super User) and ended up downloading EasyBCD and changing the boot drive to C:\, cause it was set as I:\ (the system reserved partition on HDD2). Which also might explain the BOOTMGR Missing errors when I took out HDD2, cause it was looking for I:\ to boot from, but couldn't find it and didn't bother looking for it on the OS Drive (bit stupid imo). I'm 90% sure when it changed the boot drive to C:\ it told me it would repair any BCD or BOOTMGR errors it found. So once I had done that, I thought "awesome, I'll be able to clone and upgrade now". So I quickly restarted and took out HDD2, just to check it had worked and...no. It came up with a different error this time.
An operating system wasn't found. Try disconnecting any drives that don't contain and operating system.
Press Ctrl+Alt+Del to restart
So naturally I googled it, but could only find the error from people with W7, which was weird. But came to this Windows failed to start and can't find operating system Solved - Page 3 - Windows 7 Help Forums and did these and a few other bootrec commands in cmd from the repair disc
They did not work.
bootsect /nt60 C: /mbr
So yeah, I'm stuck. If you have read all of this, thank you so much. Sorry it was so long!
Just remembered, I also tried 'System Restore', but that didn't work. Just spat out error 0x8000ffff.