I only know how to make HDLOADER and PS2-Linux work on the same HDD by following these steps - (1) format HDD with HDLOADER (you don't have to store any backups at this time, just format), and (2) run ps2fdisk (not fdisk) to create the Linux partitions (this is part of my installer which it seems you were unable to get to work for you). ps2fdisk is required because it "understands" APA partitioning. Keep any Linux partitions within the first 137GB. HDLOADER 48-bit can go beyond 137GB (up to 1TB).
I do not know how to get from where you are to where you need to be without following the above steps. That does not mean it is impossible, it just means I don't know how.
Last edited by deba5er; 02-22-2012 at 10:07 PM.
PS2 v9 NTSC, PS2 v12 NTSC, PS2 v15 VESA