Since it seems we're going to use system time tampering in our runs, I did some tests with the clock tower and it appears that the moment you create your save file, the arms default to "9 o'clock" and start ticking forward. This means that we could predict when we are going to reach the clock tower, calculate what we need to change the time to and make the changes during one of the cutscenes.
I tested this by adding "-l zu_library" to the launch options, which places Gomez outside of the library (adjacent to the clock tower - starting in the clock tower makes the clock hands freeze) when you start a new game. Digging through the code confirms that save creation time and the clock arms are tied to each other.
If anyone wants to go have a look at the game's code or anything, here's a relevant GameFAQs thread: http://www.gamefaqs.com/boards/945079-fez/66110193
I tested this by adding "-l zu_library" to the launch options, which places Gomez outside of the library (adjacent to the clock tower - starting in the clock tower makes the clock hands freeze) when you start a new game. Digging through the code confirms that save creation time and the clock arms are tied to each other.
If anyone wants to go have a look at the game's code or anything, here's a relevant GameFAQs thread: http://www.gamefaqs.com/boards/945079-fez/66110193