Here's something to try...
If your Mac Pro has issues with booting from USB but will boot from a DVD, create a DVD from the USB installer. If you know how to do this then ignore the rest, grab a dual-layer DVD and get cracking. If not, read on...
First, mount your USB installer and then go to Disk Utility. Highlight the partition Install OS X Yosemite on the upper left pane then go to File > New > Disk Image from "Install OS X Yosemite". Select DVD/CD master as the image format then hit the Save button when you're ready.
After a few moments you will have a disk image with the extension .cdr. This should be listed in Disk Utility on the lower left pane - highlight it and select Burn. You will need a dual-layer DVD for the burning operation.
If you can boot from the original Apple installation discs you should be able to boot from your newly created DVD, and hopefully it will appear as a boot option. Be warned, booting from the Yosemite DVD will take a small eternity, the installation itself will take quite a bit longer. Still, it's better to get there slowly than not at all ;-)
Alternatively, if you have a spare hard disk you could clone the Yosemite USB installer partition onto that using Disk Utility's Restore function. This should in theory be much quicker but I've not tried it out yet. I have had a successful boot and install from DVD on a MacBook (school's out for Easter so no access to a Mac Pro at the moment) so at least we know it's possible to create a working DVD installer.
Small addition - when installing from DVD the progress bars will lead to you to believe it's actually going to take forever, if not slightly longer. However, these do tend to stick at certain points while the system's busy and the whole process should be done in just over an hour.