Start with a completely empty save slot.
!!!DO NOT SELECT THE SAVE SLOT YET!!! The slot should say <empty save>. If it says ANYTHING else, it is not an empty save.
Set the system clock to 11:59:55 PM. The date doesn't matter.
!!!THIS IS THE MOST IMPORTANT STEP!!! You need to CREATE (not start new game) the save file at 00:00:00 or 12AM or Midnight. You can be a few seconds off, it's not that big a deal as long as its at midnight. A save file is CREATED when you SELECT and empty slot in the file select screen. It doesn't actually matter what time it is when you select "start new game" because you will be changing the clock anyway. The times you change the clock to are based on the assumption that the save file was created at 00:00:00. So screwing up this step will also screw up everything else.
(These next parts can be done at any time, but I will explain the best way to do them without wasting time) As the game is zooming in during the intro, quickly set the date to the next day and set the clock to 05:40:00 PM. Play through the starting part up until the game "crashes" the first time. Once the FEZ logo screen appears and the game starts to zoom in again, prepare the time change box to set the time to 06:15:00 AM for the same day. DO NOT HIT ACCEPT AND DO NOT CHANGE THE TIME YET. Leave the time change box open until you get to the clock tower in game. If you played fairly well, there should be at least 2 cubes waiting for you when you get to the clock tower. After you collect them, hit accept on the time change box and the last cube should appear. (Note: I'm sure there are tons of other times that work for these cubes, but these are what I use and they work)
There is no point trying to manipulate the system time for the minute cube. It will have spawned by the time you collect the other cubes for sure, so just wait it out. DO keep an eye out for it though because you only have a couple of seconds to grab it before it DE-spawns and you have to wait again.
It is impossible to have the weekly, daily, and hourly cube spawned at the same time.
