Boot issues every update

Hello,

A couple of things to consider:

is the BIOS version since when the motherboard was released and there are updates that you should consider GA-Z87-HD3 (rev. 1.x) Support | Motherboard - GIGABYTE Global
But make sure you update the right BIOS for your motherboard version.

From your description is seems like each time there was something during the update that somehow leads me to conclude at corrupted packages. Download is slow?
I also see that you still have the iGPU connected but not used so is better to disable it from BIOS.
For Gnome, when comes to Nvidia GPU and drivers i noticed that enabling early KMS makes things better.
See here:

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