the important parts to read from a syscheck are :
Official IOS
IOS58 (you have it, so it's good for most if not all homebrew)
cIOS Hermes type: (old, not used a lot anymore, unless you need one for musical games)
IOS202[57] (rev 65535, Info: hermes-v5.0): Trucha Bug, NAND Access, USB 2.0
IOS222[38] (rev 4, Info: hermes-v4.0): Trucha Bug, ES Identify, NAND Access, USB 2.0
IOS223[38] (rev 4, Info: hermes-v4.0): Trucha Bug, ES Identify, NAND Access, USB 2.0
Copy of IOS36 patched with trucha bug restored
IOS236 (rev 54321): Trucha Bug, ES Identify, NAND Access
cIOS d2x type : Actual important cIOS to use with USBLoaders
IOS249[56] (rev 21005, Info: d2x-v5): Trucha Bug, NAND Access, USB 2.0
IOS250[57] (rev 21005, Info: d2x-v5): Trucha Bug, NAND Access, USB 2.0
Bootmii and Gamecube IOS.
IOS254 (rev 65281): BootMii
BC v6
MIOS v10 (DIOS MIOS 2.6.1+)
I doubt you really followed the guide you linked, because you don't have the expected files and versions.
Look at the d2x cIOS, you currently have "version 5" installed, while the guide tells you to choose between v10 (beta52) and v10-alt (beta53)
You need to update to at least v8 (or v10 if v8 is not working).
v8 = latest official release
v10 = beta, but stable. adds more HDD compatibility
V10-alt = beta, stable but less compatible. Allows USBPort0 and USBPort1 to be used by USBLoaders. All other cIOS version need to connect the drive to USB Port 0.
use this installer to get ALL the versions:
http://www.mediafire.com/download/5ggh53tj9hhp1tr/d2x-cios-installer-3.1-v6-v7-v8-v10-wii.7z
install v8. (don't bother with v10 if v8 works)