No matter what guide you follow, remember THESE rules if you have a dual-cpu Mac Pro 2009 (they came without IHS heatsinks on the CPUs):
* You MUST flash to firmware 5.1 BEFORE you switch to newer CPUs, or the system will be unbootable.
* You MUST raise the heatsinks by 2.2-2.5mm via washers so that you avoid crushing the CPU and destroying your motherboard.
* You MUST NOT overtighten the screws, even when using washers! Hand-tighten them very gently and don't be afraid to leave a small gap between the heatsink and the washers; even the stock machine has a small gap between the heatsink and the pegs/posts. Your washers are just your emergency-rescue against idiocy! What matters is that you tighten with the CPU LID as your tightness reference, NOT the washers! Just a couple of turns will hold the heatsinks in place. You don't want to crush the CPU!
* You MUST cut out room for the fan connectors, because if they don't connect your Case fans will run at 100% speed to compensate for what it thinks is a dead CPU-fan.
* You MUST add extra-thick thermal strips for the voltage regulators, so that the heat they generate transfers to the heatsink.
* Do NOT attempt to remove the IHS (integrated heat spreader) "lid" on your Xeon CPUs. They are workstation CPUs with SOLDERED lids (directly onto the cores) that CANNOT be removed using common de-lidding techniques and you'll kill your processor. Even professional electrical engineers with heatbeds have destroyed these CPUs while attempting to remove the lids. Also note that unlike consumer-CPUs, the soldered server-level Xeon CPUs do not benefit temperature-wise from de-lidding because the heat-contact is already practically perfect thanks to the tight soldering. So keep the lids on and follow the above 5 rules!
* If you install faster RAM, you MUST perform a PRAM reset to re-setup the system to enable the faster speeds. You don't need to do this step if you aren't changing RAM.
Fail to do these things and you WILL **** things up. Don't be an idiot.
Here are the parts required to upgrade a 2009 Mac Pro 4,1's CPUs:
A firmware upgrade to Mac Pro version 5,1, to add support for the new CPUs. Must be done BEFORE swapping the CPUs. Do it carefully and don't interrupt the flashing process. See the first post in this thread for the download (you must be registered to see the link).
1-2x New CPUs (of course).
1x Silicon Thermal Pad, of 3-3.2mm thickness for extension or 5mm for total replacement. Get 10x10 cm pads so that you have room to cut out the two strips you need (each strip you need is ~10cm long but not very wide). Many people that do this mod get 2mm pads but that's WAY too THIN and will leave airgaps, especially after compression, so DON'T use that or you won't sufficiently cool your voltage regulators meaning your system might die within a few years of use! Get 3-3.2mm pads, and just lay the 3mm thick pads on the voltage regulator chips, and they'll bridge the gap to the existing pink 2mm pads on the heatsinks. Some people try to find 5mm pads for a total replacement, but that's nearly impossible since it's a very uncommon thickness, and it's also more difficult since it requires gluing the new pads to the heatsink. The good news is that stacking a 3mm pad on top of the voltage regulators works perfectly and provides practically identical thermal transfer thanks to them being packed tightly together. I chose a 3.2mm pad of real silicon, which compresses itself to the perfect size and bridges the gap tightly. It's better to get a thicker pad than a too thin one which leaves airgaps and provides insufficient cooling! If you are patient and ok with waiting for 1-4 weeks, I recommend this chinese seller with free shipping: 3mm silicone pad. Whatever you do, be sure that you buy REAL silicon pads to transfer heat the best. You don't wanna fry the voltage regulators and need a $400 repair in your expensive machine, just to save a few dollars on cheap, ****** non-silicon thermal pads! People have killed their machines after 1-2 years of use with thin/cheap pads; so again, my recommendation is a ~3mm thick REAL silicon thermal pad, stacked on top of the voltage regulators, so that it compresses nicely and perfectly bridges the gap.
1x 3mm Hex/Allen wrench, OR a Torx T15 screwdriver/wrench if you can't find a Hex wrench, either one of them works and have the exact same dimensions. It needs to have a thin shaft of at least 7.5cm length so that it fits all the way down. And use a screwdriver that's not thicker than 5mm along the shaft, meaning that those interchangeable "bit-sets" are way too wide to fit into the heatsink holes.
1x Thermal paste for the CPUs. Most people have no imagination and just go with "Arctic Silver 5", but there's lots of equivalent brands on the market:
http://www.pugetsystems.com/labs/articles/Thermal-Paste-Roundup-172/ I picked the Gelid GC-Extreme. Choose whichever one is in stock!
16x 1.1mm-thick M4 washers (it simply has to fit on top of the M4 bolt which is 4.1mm inner diameter so anything with ~4.4mm inner diameter is good), and most importantly 1.1mm thickness. You need two for each cooler post, 4 posts per CPU; and you must be completely sure that they add ~2.2mm height total (absolutely not any higher than 2.5) to completely protect the CPU during tightening! In my case, I could actually only get 0.8mm washers so I ordered 24 instead and put 3 on each pad for a total height of ~2.4mm which is extremely close to the exact height added by the CPU's IHS (heatspreaders/lids). Another guy did 2.5mm with no problem, but don't go higher! Use calipers to measure that you have reached the intended lift level. See below quote for the exact size to aim for:
