The thing I'm most confused about in all of homestuck is the machines at the beginning. What order do you use them in and what does each one do?

Really? The equipment? That’s like Homestuck 101. I think Rose goes in detail in her GameFAQ, but like. There’s the Cruxtruder. It has the Kernel for you to prototype, you bonk it open and start to produce Cruxite Dowels. It also displays the countdown to see how much time you have left. You just need this to get the Dowel. Then you take the Pre-Punched Card, and the Lathe- When you insert the card, the machine recognizes the pattern on it and creates a distinct and unique pattern with its spike thingies. You put the Dowel on it, and it carves said pattern on the dowel, making it into a Totem. Then you shove that Totem in the Alchemiter, and the scanner reads the grooves the Lathe made and goes like, “Oh! This coincides with X captcha code, which is this specific item. If you want to make it, you need X amount of Grist”.