Here's how to fix the time issue. Problem is by default Windows saves the time to the hardware clock in local time, but Linux saves it as UTC. You can make Windows also save it as UTC by changing a registry setting:

For 64-bit Windows, open regedit then browse to HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\TimeZoneInformation. Create a new DWORD entry called RealTimeIsUniversal, then set its value to 1. Reboot the system. The clock should now be in UTC time.

Switching between Windows and Ubuntu led to a weird time difference on Window’s part (it still does)

Google how to set your windows clock to UTC. You can maybe do the reverse and set linux to localtime, but I find it much cleaner that the system clock is in UTC as it's an objective and stable standard, unlike localtime which can change with daylight savings or if your move.

There are many ways to run code at startup. cronjobs and systemd are common ways to handle this. I have also had things start automatically with my desktop environment which comes later in the boot process.

Fingerprint sensor stopped working

File an issue to libfprint, your fingerprint reader probably isn't supported yet.