The link is a good summary of what's easily available at the moment. All three options there can autoboot TWiLight and I think should be able to be used with the kernel, though I think only YSMenu is supported for kernel loading from TWiLight on the DSONE, not EOS. Just avoid the DSONE clones unless you have Unlaunch installed as they won't work on DSi without it.
Also, just in case you haven't already, have you tried using a different SD card? DS flashcards tend to be fairly reliable from all I've seen, but it's not uncommon for an SD card to just kinda die so it could actually be that your flashcard is fine and it's just the SD that died. I'm sure they do die occasionally though...