Why jump through the hoop of making a .3ds file and then converting to CIA? Homebrews can be compiled directly from ELF -> CIA. You just need to use makerom.
Something like this (note that copy pasting here is pointless, it's just an example, so don't bother):
Code:
arm-eabi-none-strip program_stripped.elf
makerom -f cia -o install-me.cia -rsf cia.rsf -target t -exefslogo -elf program_stripped.elf -icon icon.icn -banner banner.bnr