BOOTMGR missing usually means the bios has loaded the primary bootsector code that usually then reads the BOOTMGR into memory and executes it , normally USB boot required additional bios code to keep the drive listed as a fake IDE which the bootsector loader would access bootmgr via and once thats done it hands over to bootmgr. Now without bios support you wont get usb boot unless you start using more advances boot loaders like grub which does support usb boot in the bootsect code last time i checked.
As for cloning the drive you should try booting clonezilla and choose ram loading, this will allow you to swap to your backup drive when you ready to clone and allows you to see whats installed prior to adding the usb drive making the possability of overwriting your real drive lessened.
This will also allow you to test usb boot as the clone zillausb flash image (can be written to a flash via windows using rufus flash writer 3.4) uses grub and/or syslinux (another system support usbboot) and also support the various flavours of sector size that the system might need.
it's possible to also test the cloned drive in a virtual machine (qemmu is best for windows & direct drive access) and via clonezilla compare mode. Clonezilla itself will also allow some editing of the usb parameters for the clone like sector size, expanding of the partitions, it is also very good at doing 1:1 clones due to linux kernel drivers being better at low level than windows in some cases.
darkspr1te