Mac Pro Rebuild / Upgrade Options - Mac Pro 4,1
2009-era Mac Pro 4,1 systems can be upgraded to 2012 Mac Pro 5,1 specification and beyond to support hex-core CPUs and faster RAM, SSDs or PCIe-connected hard drives giving you 12 cores and really fast storage. Ten-year-old systems with a little loving upgrade can easily run macOS 10.14 Majove, and in some cases run it faster than the 2013 Mac Pro 6,1.
The Mac Pro 4,1 and 5,1 do not support MacOS 10.15 Catalina natively although there is already a workaround to bypass the installer restrictions. At the time of writing this, Catalina has a large number of 'issues' in general even with supported hardware so this may not be something you want to run anyway. The sweet spot for a Mac Pro 5,1 appears to be running 10.13 or 10.14 so stick with that. 10.14 Mojave of course requires a Metal compatible graphics card which will set you back at least a coupe of hundred dollars currently.
Upgrading Hardware - Mac 4,1 systems
YouTube 12 core Upgrade
Upgrading the CPU in a 2009 Mac Pro
Upgrading a 4,1 2009 quadcore 2.93 Mac Pro
2009 Mac Pro 12-core CPU Upgrades
There’s a ton of YouTube videos to walk you through the process and many articles on the subject so don’t just take my word for it.
Depending upon whether you currently have a single CPU (4-core) system or a dual CPU (8-core) system, you have different CPU options. These are the ultimate:
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Single: Intel Xeon W3690 3.46GHz SLBW2 6 Core Processor LGA 1366 i7-990x
- Dual: Matched pair of Intel Xeon X5690 3.46GHz SLBVX 6 Core X58 LGA1366 Processors
Here's a good article on supported CPUs and no you can't run X5687 3.6Gz or X5698 4.4Ghz CPUs in your Mac Pro. You can however run X series CPUs in a single CPU tray.
At the time of writing this, a pair of Xeon X5365s seems to be the sweet spot financially - although slower than the X5675, they run at the same speed of the X5690s but lack turbo boost but cost less than half the price of the X5690s even if you can find a pair for sale on Ebay or elsewhere on the second hand market.
At the time of writing this a W3690 sells for about $50 on ebay and a pair of X5690s for $100. If you are prepared to go slower to 3.33Mhz a W3680 can be had for under $40 while a pair of X5680s can be had for under $85 or a pair of X5675s for $50.
If you have ever changed out a CPU before then upgrading a single Nahalem CPU to a Westmere will be a piece of cake. Unscrew each of the 5 hex bolts a little at time so you don't warm the components. Do the same on the reassembly. Do not not over-tighten or your system will not boot. A good CPU heat paste and a spreader is a pre-requisite as will cleaning materials to remove old paste.
A dual CPU setup is a different story however. Apple designed the Mac Pro 4,1 dual CPU tray to use lid-less X series CPUs so that the heatsinks connect with not only CPUs but also other components of the processor board. While you could pay someone to de-lid your purchase or pay more for lid-less processors, the cheapest way is to purchase a strip of heat conductor padding and place this to connect with the processor card components.
You will also need a 3mm long handle Hex wrench in order to remove and replace the heatsinks. Be careful not to over-tighten when using lidded CPUs. Heatsinks should be tightened down thumb tight or your system won't boot. If you have issues, install CPU A first and test then install CPU B.
NOTE
If you have the 2009 version of the Mac Pro and have not upgraded to the 5.1 firmware yet, you will need to download and install the 4.1 to 5.1 firmware BEFORE installing these CPUs or they won't work! (See the next section for details)
A couple of points to bear in mind: In addition to upgrading 2009 firmware before upgrading CPUs, MacOS 10.12 'Sierra' also requires that you also upgrade the stock GT120 video card(s). It is possible to use this card afterwards but in my experience, not for the OS install.
An ATI Radeon HD4870 was available as an upgrade option for the Mac Pro 4,1 so if you have one of these you may be good all the way to High Sierra and the Mac Pro 5,1 came by default with the even better ATI Radeon HD5770 with the ATI Radeon HD5780 as an available option. All these cards are good till you get to MacOS 10.14 Mojave which requires a Metal capable video card.
So what are your options? Obviously an Apple Radeon HD if you have one or can borrow one would be best for all the upgrades as it allows you to view EFI boot screens. A Windows / Linux card will not.
If you intend to install MacOS 10.14 Mojave or MacOS 10.15 Catalina then you really need a Metal capable card. That probably means that you need to flash a non-apple card with the Apple EFI firmware if you want to see boot screens, or like many others you could just keep your legacy apple card around for troubleshooting if needed and blind boot. There are fixes for both Mojave and Catalina to run on non Metal cards but in my experience your system will be slow.
Be Warned
You will need to upgrade from OS X 10.11 incrementally to get to the latest version of MacOS. Simply building a USB installer stick for MacOS 10.14 WILL NOT WORK.
Each upgrade installer reaches out to Apple to download additional components spme of which are machine specific and others of which are firmware upgrades. If you miss a firmware update you will have to come back and repeat the process again. Yes, it takes a lot of time updating, installing and patching.