Joe, in order to properly wire a machine shop, an electrician has to go well beyond his apprentice training- and he must understand the plant's operations. There must also be plenty of HONEST communication between the plant folks and the sparky.
Simply put, considering the typically poor job archetects do in laying out a simple restaraunt, the very real complications of a production facility shold not be ignored.
As an example, I recently wired a plant with essentially a blank print- no equipment layouts, nothing. Yet, this was a customer, and a process, with which I was familiar- so I was able to "guess" right on all but two small items. Even so, I had to deal with a LOT of second-guessing and doubting Thomas's during the job; only after they moved in were they able to see that I was well "ahead of the curve."
Enough bragging, though- here's where you start: layout the equipment so machine "A" feeds machine "B". Allow plenty of room for material handling, scrap handling, and traffic. Keep in mind where the inspection tables and tool chests will be.
Lay out the lighting so that you get LOTS of light- think "bright" and double it (quadruple it if you've been doing mainly warehouses)- to the surfaces of work tables and access hatches of the equipment. Light quality is at least as important as the number of ft-candles. Directed light is fine- the aisle five feet away can be considerably darker. There is NO advantage in having everything laid out in a neat grid on your plans; far better that the light be where it's needed, and the fixture where you can get to it (to change a bulb).
You treat every machine as "continuous" to size your supply wires (feeders). Here is where you have to decide- pipe or bussways? Remember, things will get moved or replaced in time.
You will also want to plan for data drops to every machine; the days of some guy standing at the machine, with a print stuck to the cover, and his hand cranking a handle are LONG gone. Don't ignore "physical protection;" the area will see a lot of action!
Every machine back and work station will need to have a convenience receptacle. I have lost count of the times I've seen such receptacles added later, usually by tapping one of the supply legs and using the pipe as the 'neutral.' Don't set the stage for this to happen!
Don't overlook the other things that will be necessary- the air compressors, the garage door openers, the exhaust fans, etc.
Then there is the matter of power quality. It is very possible that you will be adding a capacitor bank to correct "power factor." There are also real advantages to having some means of "cushioning" spikes from the PoCo supply, be it a UPS, battery bank, even transformers. In all cases you should have protection against single-phasing.
While many of the newer machines have these features designed into them, don't rely on that. Often the air compressors will be quite basic- and compressed air is a "utility" for these machines.
