I used GM9 and followed the instructions to a T, I believe. I actually had the episode 1 patched so I tried to use that one again, but it gives me the partition error. I tried dumping a clean version of it and that one gives me the font corruption error.
I dumped the eShop version and yes, I have more than 2GB. I have two files. One tells me that the font is corrupt and the other says that Partition 2 had an error patching. I don't get the update CIA at all.