Are you using menuhax or arm9loaderhax? Your signature would imply the former but anyway
Both cases:
1. Make a folder called D9Game on root
2. Place the .cia of the game in that folder
Menuhax:
3. Get Decrypt9WIP.3dsx in /3ds/Decrypt9WIP (that is to say - make sure you have Decrypt9 in your homebrew)
4. Access homebrew on sysnand (so before booting to emunand) (because you need arm9 access)
Both:
5. Open Decrypt9 (on a9lh this would be done by holding Start if you followed Plailect's guide btw)
6. Go to Game Decryptor Options
7. Select CIA Decryptor (deep)
8. Wait till done. .cia will be replaced with decrypted version
9. Get decrypted .cia to PC
10. Use ctrtool to extract romfs and exefs following ihaveahax' guide:
https://github.com/ihaveamac/3DS-rom-tools/wiki/Extract-a-game-or-application-in-.cia-format
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It may seem less convenient than using braindump but in reality it is a LOT better both for quality and hassle.
As for you using FTP to transfer files - I actually highly recommend you either keep the screws unscrewed or take them out all together. The lid stays on perfectly fine without them. Trust me when I say it's a huge hassle to always use FTP.... I know the feels when doing basic romhacking...