Did you repack TMS#FE using -encryptKeyWith <Wii U common key> ?
And yeah, it was kind of annoying to use the 64GB SD, but in the end it worked out ok and I've got everything I want installed. If you need to get a new card for the Wii U I'd say buy a 128GB, but if you have a 64GB laying around and want to save some money it will work fine (as long as it's Class 10/UHS-I).
One thing that didn't occur to me until the very end is that you can probably pop out the SD card while at the WUP Installer menu and replace the files in the install directory with different games, then put it back in and keep going. Should save the time required to shut down/restart/reload Mocha CFW over and over. It just requires you to have downloaded everything you want to install ahead of time, which leads to another tip: if you buy a Wii U, go ahead and download everything you want from uTikDownloadHelper now so you have all the files ready to go on your PC when the console arrives.