this is mostly bad info. between the 2008 and 2009 releases, there were significant changes to the CPU and system architecture. the 4,1/5,1 systems are definitively better than their predecessors in every way imaginable. you can keep investing in your 3,1 but at some point you are just putting more racing strips on a Ford Fiesta.
now, if you intend on heading down the route of upgrading and modifying a base model you need to understand what you are getting into and arm yourself with knowledge. there is a lot here in these forums. there are also a lot of tinkerers who like pushing.
for the most trouble free process, find an original 2.8Ghz quad 5,1 and made the following mods:
- CPU, a
X5690 SLBVX. (6 cores with hyperthreading will beat up any 3,1)
- RAM, 3 X 16GB (for 48 total)
- GPU, flashed Radeon R9 280X ( two mini DP, HDMI, DVI).
if you want to spend more, you can go for a dual CPU and 12 cores. but one or two, get a 5600 series. if you want an Nvidia (CUDA) card, just make sure you understand the implications of that.
drives, SSDs. you have 4 bays with sleds (similar to your 3,1) and you now have 2 positions in the optical bay htat can be well used with the right
adapter.
PCIe cards:
- the most valuable will be USB 3. I recommend a card like
this, that has a discrete controller for each port. cheaper cards share one controller between all ports, making port to port transfers significantly slower. hopefully we will soon see cards with USB C 3.1 ports that are Mac compatible.
- there are also a variety of kits and cards to put an SSD in a PCIe slot.
a word of warning. yes, everything is used part off of eBay and these parts are only getting older. so approach with caution. I can offer that I've modded several Mac Pros (and more than a few Windows boxes) this way and they all performed well. but there is risk and you have to be willing to take that on. so research, learn and start trolling eBay to get a handle on what is out there and what it costs.