MacPro4,1 and 5,1 CPUs can be upgraded to 3.46GHz, 6 or 12 core depending on whether you have single or dual CPU model. Also, when using 130W TDP CPUs in dual CPU models, fan profiles should be changed to avoid uncomfortably high CPU temps. This, of course, will add noise.
When upgrading video cards, you can use pretty much the same video cards as hackintoshes. The only difference is that unless you your video card has Mac specific EFI firmware, they will not display any video until the drivers are loaded. This means you can not access the Option boot screen used to select boot drive. If using a Maxwell card in El Capitan, you MUST set nv_disable=1 or it will kernel panic.
In my opinion, unless you have have apps that can make use of 12 cores/24 threads, a modern Skylake or Kaby Lake system makes much better sense. The run cooler, use far less power, and have much, much better single core performance.
As much as I loved my old Mac Pro, it became increasingly difficult to mask its age. In trying to modernize it with USB 3, SATA 3, and M.2, I ran out of PCI-e slots and had to choose which to remove to make room for my 10GbE card.
Again, this is all just my opinion and there are still many people who find their Mac Pros perfect for their needs.
