bootmgr missing when installing windows 8

Are you sure, the usb stick is part of the boot order in bios?

To use the Windows 7 USB/DVD Download Tool, you will need to first ensure that you have access to an ISO image file of your installation media. Once you have an ISO file of your installation media, you can simply run the tool, which will ask you to point to the .iso file, and have it create bootable media on a USB device. The Windows 7 USB/DVD Download Tool is only compatible with Windows installation media. The Linux distribution you mentioned may have an entirely different boot process which is incompatible with the tool.

Lastly, one of the most common errors with installing Windows from a USB stick on many modern systems is the use of a USB 3.0 port. The drivers for these ports are not present in the setup environment on the installation media and thus the boot files are not detected. If your media has been created correctly using the Windows 7 USB/DVD Download Tool, you may simply wish to try it in a USB 2.0 port.

Beyond what was described above, an alternate method for creating installation media for your system would be to use the deployment technologies available from Microsoft for administrators and IT professionals to deploy large quantities of Windows to systems in an organization. The Microsoft Deployment Toolkit (MDT) installed on another workstation would permit you to import your installation media and create a customizable installation interface on a USB stick. Furthermore, it offers the ability to automate installation of applications, configure settings, automatically install drivers both in the Windows Preinstallation Environment (Windows PE) and in the deployed operating system, and quite a bit more. With a Windows Server with Windows Deployment Services (WDS), it even supports PXE boot where you could boot your PC directly from the network with no local media and perform the installation directly over the network from the Deployment Share.

For more information on deployment technologies offered by Microsoft, check out the video Alphabet Soup Deployment: Understanding MDT, WDS, MAP, ACT, SCCM, and USMT. The Windows 8 Deliver and Deploy page from the Springboard Series on TechNet provides even more information including guides for using the various deployment technologies, videos, walkthroughs, and more.

The partitioning of the SSD would be done once you enter setup for Windows 8. That should not be the issue.

Are you connecting to the USB ports on the rear of the computer (directly attached to the motherboard)? This would eliminate the possibility of the case components or USB ports being responsible. Bear in mind, only the two black USB ports which are beside the blue USB 3.0 ports under the PS2 keyboard and mouse ports are USB 2.0.

Is the USB Stick at least 4GB? My bootable USB stick with the Windows 8 installation files is 3.51GB and was created using the same tool.

Testing another USB stick is a good idea. Another thing you could try is creating a DOS boot USB drive. There are instructions in this TechNet Blog post which you could use. If that boots, it is the media creation process, if it does not, it is the boot configuration of your system or the USB stick itself.