To begin with, the Mac Pro had a pair of slower CPU's that I seem to have misplaced (I am writing this after the fact), but I do know they were clocked at 2.0 GHz. Not bad, but could be far better. 3.0 GHz kind of better. Additionally, the RAM could use upgrading from 2 GB to 10 GB, as could the graphics card. I was planning on using the GPU from my Windows PC, but that will all be explained later.
First, and easiest, is the RAM. There are two riser cards, card A and card B. As far as I can tell, they are electrically identical and thus interchangeable. However, the RAM has to be installed in a specific order, as per this picture which is (upside down) on the door of the system.
And here is a picture of the riser cards as they came installed.
So the top card (A) is on the right, and bottom (B) is on the left. You'll notice a discrepancy here. Installed in card A are the four 512 meg sticks with Apple heatsinks that it came with, not installed in accordance with the instructions. Odd, but it showed 2 gigs in the system report, so I wasn't going to question it. BUT WAIT, THERE'S MORE! The two silver heatsinked sticks in riser B are each 4 gigs. The genius that owned the system before me had upgraded it wrong, so it only showed 2 gigs total, but actually had 10 installed. Nice, now I have 18 total gigs that I hadn't planned on. So I reordered the RAM to have the newer 8 gig sticks in slots 1 and 2 of each riser card, and the 512 meg sticks in slots 3 and 4. If you do something other than this, make sure you install the RAM in matched pairs according to the side panel. I left the riser cards out for the next bit of installation, just to make it easier on myself.
Next up were the CPUs. Getting access to the CPU's is a bit of work, a result of the "beautiful industrial design" that Apple loves so much. There is a metal panel of sorts that sits in the way, seen right here:
However, you will notice that I have already removed it, which was a royal pain. I had to unscrew the two screws you can see in the RAM cage to give me enough wiggle room to get it out. Also, a handy peice of information that I could not find anywhere on the internet for the life of me was that the whole fan cage assembly, that grey box on the left, slides right out of the case. I didn't find this out until I had already removed the silver panel. The way I should have done it, and the way I would recommend you do it, is:
1] Remove RAM riser cards A and B
2] Loosen the two screws in the riser cage, seen below. Don't worry about loosing them, they're captive.
3] Take out these little screws here, they're not captive and will get lost if you aren't careful.
4] Slide the whole fan cage assembly out, wiggling the silver panel away from the RAM cage as you go. It'll be a little stiff, so just take it slow, and you might need to take out hard drive bays 1 and 2.
You can do it other ways, but you're likely to end up with a cut finger like I did.
Anyhow, being Apple, they couldn't just let you use a regular allen wrench for the absolutely humongous heatsinks they slapped on there. You'll need a really long one, or a longer screwdriver with changeable heads and a smallish hex bit. The screws are located down in the holes on either side of the heatsinks (there are eight in total, four to each heatsink. I don't know how single CPU systems are laid out). Again, these screws are captive, which is awesome.
If you did it the way I described above, the fan cage will be gone. If you didn't, you'll wish you did because it has to come out next to get the heatsinks out. Here I have removed both heatsinks, the fan cage, and one CPU. This gives a pretty decent view of the surrounding area.
The astute among you will notice that I have moved the plastic bit in the drive cage. It's not necessary, just something I did when trying to remove the heatsinks without taking out the fan cage. It didn't work. Next up I cleaned off the heatsinks (and the old CPUs too), and reassembled the whole disaster (of note, I used the Xeon x5360 3.0 GHz CPU's, found on ebay).
I used Arctic Silver thermal paste. It's a bit spendy, but worth it on an old machine that puts out a lot of heat. Here's a fancy picture of it, along with the cleaning chemicals that I got. You can honestly just use Isopropyl alcohol (found at walgreens or your chosen pharmacy) instead, as this was pretty expensive too.
If you've never upgraded Intel CPU's before, there is a small metal lever held in place by a small metal catch. Push it down, then out, and lift it up. The metal bracket should come up easily. When installing the processor, you must line up the gold arrow on the CPU with the notch / arrow on the plastic holder. It will only fit in one way, and it won't close right if you force it to fit incorrectly. Put a little dab of thermal paste on it, then seal it up. Various people on various sites will tell you that the thermal paste must be a certain size, shape, whatever, but it doesn't make any appreciable difference. No really, see for yourself. Reassemble everything in the opposite order you took it apart, making sure to remember any small screws.
The graphics card is the easiest part of this, just make sure to google "[your graphics card] mac pro compatable" to see if it is supported by the nvidia web drivers and what Mac OS you need. I will go more into drivers in the next post.
I had a choice of two graphics cards (read: I had a spare lying around and one in my PC): an nVIDIA GT640, and an nVIDIA GTX 750ti. These are both nVIDA EVGA licensed reference models, which is apparently important for cards of certain architectures (I think it only applies really to maxwell cards, but just buy a card that uses the reference design. A quick google search would serve you well in this respect).
I've also heard rumors that the port arrangement matters as well, but I don't have enough cards to test this theory. From what I've seen circulating around the web, any old PC compatable PCIe card will work fine, but you can get it flashed through services like MacVidCards to get a boot screen, or you can do the bodge that I've done. Anyway, it's easy enough to put in a new graphics card. This picture was taken after installation, but it will do for explaining.
On the far right, you'll see a bar with two (again captive) thumbscrews. Take these out, and the bit of metal they're attatched to, and set it aside. Then look at the back end of the PCIe slot that the card sits in, and locate a small, black, plastic lever. To remove a card, pull this lever up gently, and rock the card back and forth out of the slot. To put a new one in, just line it up and push until it is seated, and reattatch the metal bit. Make sure to remove any of the small slats that cover the extra card slots at the back and keep them for later (you never know). I've chosen to put my 750ti in slot 1, and the original GeForce 7300 in slot 3 so I can have a boot screen. I chose slot 3 because it gets 8 PCIe lanes as opposed to the 4 from slots 2 and 4. The easiest way to make the boot screen trick work is to plug both cards into one display, set your display to accept input from the original card, boot the computer, then do whatever you need to do (like choose the startup disk) and let it boot. Once you're into the OS, you can then unplug the older card and switch input to the new card. It's a massive bodge, but if you don't use the boot screen, you can just leave the old card unconnected and boot normally, you just won't have a boot screen.
Since you're done with the CPU's and GPU(s), you can put the RAM risers back in, making sure the configuration matches that shown on the side panel. Make sure you've seated everything properly, plug it in, press the power button and pray. If all goes well, you'll be at your login screen in no time. Login, and check the 'About this Mac' dialog.
If you used the same CPUs as I did, you'll notice that it doesn't recognize them. This is due to the fact that the Mac Pro 1,1 was built before these processors existed. The 2,1 doesn't have this problem. I'll explain how to fix that in part 3 of this series. The main thing you want to check is the RAM.
This is the easiest to screw up, as it really does matter what order you put the RAM into the slots. If your computer won't boot, it is most likely the RAM (unless you have no OS installed). To check the RAM, open the side panel and watch the outermost edge of the RAM risers when booting. They have a lovely array of diagnostic LEDs sitting in the outer center of the riser cards. If one (or more) LEDs stays lit for more than 10 seconds after you boot the Mac, then try moving the matched pair to another position, or maybe the other card, making sure to stay within the ordering constraints listed on the side panel. If that doesn't work, install only that RAM, and if it still doesn't solve the problem, it's likely you have bad sticks. Do not try to mix and match the RAM, it will not work. I tried this just to see what it would do, and a lovely christmas tree of LEDs on the riser cards lit up.
Assuming you've got all of the hardware sorted, you can enjoy the system in all of its (probably low refresh rate) glory. Or, for further optimizations, you can head on over to part 3 of this guide, in which I will go over the software side of things, and post links to any (of the many) forum threads I found helpful.