Plug and play made it display the total time (10d 9h 19m 0s) in an obscure position of the screen.

Upon reading and trying to decipher the config file I have absolutely no idea how to use the 'custom pattern' syntax option as it is very poorly explained (or I'm just incredibly stupid in which case would still need to be explained better).

Is there a way to make it display like this:

12:35 Daytime (Day 3145)

Here are some examples:
https://www.curseforge.com/minecraft/mc-mods/simple-world-timer
Here are documentation on java.text.SimpleDateFormat and examples:
https://docs.oracle.com/javase/7/docs/api/java/text/SimpleDateFormat.html

For 12:35 Daytime (Day 3145) try to use
HH:mm a'(Day &d)'

Please note, that instead of "Daytime" marker you can use only AM/PM which is provided by a marker.