YOU MUST DISABLE A COUPLE OF USB CONTROLLERS.
there is NO way to change the irq sharing as it's hardwired into the motherboard and ACPI doesn't allow it. the usb thing is not a big problem and it's quite common. the graphics card is problematic, but hopefully it won't stop the show. does that motherboard only have 2 pci slots? if so, the your only choice is to disable the usb controllers that share with those 2 slots and hope for the best. if you have 3 slots, you can move the two cards around and see if you get a better configuration.
another thing that might help is to go into the bios and disable any ports or onboard devices you don't use such as onboard sound and serial and parallel ports. this might free up enough irqs that some of the sharing disappears.
SLI motherboards are designed for maximum video performance, not maximum pci performance. plainer, more industrial motherboards work much better. intel motherboards and/or at least intel chipsets pretty much always work well. even still, i always have to disable a couple of usb controllers when i build systems with multiple cards. afterwards all, or at least most, usb ports still work in the same way that you can plug several devices into one usb hub into one port...