The invalid sector size warning seemed to stop after unplugging a USB hub/SD card reader, can’t say I know why exactly but I did stumble on another post of someone who had a similar issue but it was also keeping them from booting.
I managed to align my partitions correctly by doing as Fabby said, I was unable to at first because I needed to close my luks encryption before changing the start of the partition.
Haven’t got to working out what issue I was having with clonezilla but if i do i’ll update this space.