Well looks like I'm finding answers faster than anyone can answer (especially since I'm still awaiting approval for my post to be displayed publicly).. Hopefully this will help anyone who has faced the same issues.. So for the boot issue, I was missing the boot-efi partition, i.e.
'UUID=xxxx-xxxx /boot/efi vfat defaults 0 1' where XXXX-XXXX is my own boot/efi partition ID.. I am not sure why but during the upgrade from proxmox 8 to 9 it was removed....
so what I had to do is this
1) execute 'fdisk -l'
which will get you all your drives partitions and you need to find where your EFI System parition is installed
View attachment 88908
In my case it was /dev/nvme0n1p2
2) execute command 'blkid'
This will give you the IDs of all your partitions and you need to find the device you found above where EFI System is to find its ID
View attachment 88909
In my case it was EB51-AD07
3) Edit /etc/fstab
You will need to add the following to your fstab
View attachment 88910
Basically add your EFI partition using the UUID you found.
4) Reboot
After rebooting you'll need to execute the command 'update-initramfs -u -k all'
It is possible this will complain for each of your kernel profiles and tell you to reinstall grub. Just do what it tells you and then you should be fine
View attachment 88911
What an adventure right?! I hope this helps anyone who got this issue after upgrading to Proxmox 9 where somehow the boot/efi partition is removed.
As for the next issue, passing through the LSI SAS2008, I'm on something and I'll see if it works and post a follow-up here.