If you look at the rear of the MDD and the rear of an ATX case you'll see that things wont come close to lining up. You would have to make a new back for your ATX case.

For the ATX psu mod I suggest getting a power supply with a big 120mm fan inside of it like one of these (then again both these brands are total turds): chiefmax600.jpg17-163-017-05.JPG
They tend to only take up half of the case and have pretty dinky heatsinks to make room for the large fan. They fit perfectly inside of the MDD psu case. Make sure to get a 24 pin psu that has a P4 connector as well.

Then you must wire up the connector from the original MDD supply onto your franken-psu. I suggest using a P4 and 24 pin extension cable to make a sort of adapter. That way it will be sure to reach and you can reuse the adapter if you need to.

that frankenmac guide has the correct wiring. You don't need to connect anything to the +28v pin. It isn't needed unless you are using the ADC connector with an apple monitor. I'm not sure why he says it is required.