The pamac-gtk package is the appropriate GTK4 version of Pamac-Manager for GNOME. It should already be installed (pamac-gtk3 was sometimes suggested for KDE in the past, but no longer).
Some prefer yay. I use it myself sometimes.
I don’t believe the choice of package manager is the problem here. 
More likely your system was in an unsupported / unmaintained state when you updated – in those cases there can be unpredictable consequences.
With many AUR packages in the mix, that can also be a complication:
If that’s an option for you, then it’s certainly the fastest way back to a working machine.
Should you decide to do that – and presuming you will still install GNOME – I’ll add some useful links in a moment:
1. It’s preferable to install using the latest available ISO. The ISOs on the “Download” page are still the old ISOs, but you can download the currently recommended Stable ISO from:
- https://forum.manjaro.org/t/stable-update-2025-12-08-25-1-anh-linh-preview/183479#p-812260-full-9 - The new stable release is expected soon, but this is recommended for now.
2. Also recommended – Create a Ventoy USB (A new bootable USB solution)
- If the system doesn’t support UEFI, look for the BIOS/MBR instructions in the guide.
3. Important – Read through the Stable Update Announcement thread – particularly the Known Issues and Solutions section – before installing:
4. A final note – Manjaro now defaults to the btrfs filesystem:
You might prefer to still use the ext4 filesystem, in which case you must pay careful attention during install, and make sure to manually select ext4. Likewise with your preferred swap.
That should be it.
Regards.