From researching, my main worry is my motherboard being only PCI-E and the GTX 460 being PCI-E 2.0. I know that PCI-E 2.0 is backwards compatible, but I'm wondering if I will run into bandwidth issues with this GPU having only PCI-E. Other than that, I'm really not sure what weak links I should look for or expect. Thanks in advance, and just let me know if you need additional information.
The GTX460 Won't take any more power than the 8800GTX he has now (It also uses 2x 6pins), so there should be no issue there.
As far as not having PCI-E 2.0, it's not an issue as long as your PCI-E slot is running in x16 mode. It will be basically the same as having the card in a PCI-E 2.0 x8 slot, which is a 1-2% performance hit at worst.
Just avoid a PCI-E 1/1.1 x8 slot, which is only equivalent to a PCI-E 2.0 x4 slot (Anywhere from a 5% to 15% or so hit depending on the game) and the difference won't even be noticeable.