I tried CFG Loader and it worked, tried WiiFlow and it worked, and then USB Loader GX and it worked. WBFS only. No FAT32 partition or anything. I use my SD for all homebrew, so i don't mind using WBFS only with my drives. Haven't played super long or anything, but seems like all of them work just fine.
Just adjusted the "sleep timer" within the software to "never", then formatted fresh to NTFS (to get rid of the preloaded software on it). Then used WBFS Manager 3.0 to format to WBFS. Trnasferred a few games to it to test and all seemed to work ok. Then backed up my 500GB Passport to my new 1TB Passport. Took over 14 hours, but finally its done, and tested more games and still working fine.