Let me make some random guesses:
You can
dump them to SD with CleanRip then use Wii Backup Manager to transfer them to your drive.
1.
with CleanRip : go to
wiibrew website,
get cleanrip, extract it on SD, launch it from HBC?
2.
dump them to SD : dump to SD ? yeah, probably put your game in disc drive, select dump disc option inside cleanrip (if needed), choose "SD" instead of "USB" when you have the choice where to dump.
3.
then use Wii Backup Manager: Maybe that step involves using a program named .....
Wii backup manager... (get that program, launch it). If you need a guide to setup and use that program,
look here.
4.
to transfer them to your drive: you probably need to select your dumped ISO and choose "transfer to drive" from wii backup Manager.
I guess it's missing one step if you dump a disc to a FAT32 partition using cleanrip :
join all split files to make a full 4.7 GB file.iso?
MSDos command line:
copy /b part1.iso + part2.iso fullgame.iso
But you know what, maybe WiiBackupManager is compatible with split files, and you don't even need to merge them.
PS: yes, this post is full of irony, because "how to do that" was the answer. (almost, maybe missing one step)
But, you shouldn't need cleanrip, USBLoaderGX should be able to dump any games to HDD (not flash drive).
I saw you finally used HDD, so everything should work.
try using IOS58 in the loader's settings > loader's IOS option, and reboot.
if you already use 58, try using 249
Maybe knowing your format, GPT, MBR, FAT32, NTFS, WBFS, cluster size, and sector size could give us a hing why it doesn't work.
Providing the loader's settings might be interesting too.
Did you edit anything in the loader > hdd settings menu ?
something like "split size" option set to 2GB instead of 4GB?