Would you explain me what I've exactly to do to transfer the files to the new N3DS? For the first I want to try it by myself (I want to learn this, too) it would epic if you could describe what I have to do.
First thing you will need is Python 2.7. Specifically the 64bit version. Then cearp's fat16 tool to extract the encrypted fat16 file. Then use padxorer to decrypt/re-encrypt the fat16 file once done editing it. The data folder will have to have certain files excluded from it to make sure it works right on the new console. (especially since it's coming from an o3DS and is being moved to an n3DS) That part I can do for you. The files in the data folder shouldn't be too large and those you can PM me so I can get them sorted for you. The movable.sed file has to be hex edited a certain way to work on the new console without breaking it. That I also recommend doing for you.
I have a batch file that can extract, decrypt, pause while you edit the image file, and then re-encrypt and inject back into nand file after you are done editing. That file I can give you once you get all the required programs. You should PM me the files once you have them extracted from your o3DS dump. (the data folder/movable.sed file. The movable.sed folder can be found in the "private" folder)
The data folder found in the fat16 partition doesn't take up a whole lot of space. It shouldn't take you too long to upload that and the movable.sed file.
EDIT: Did you try using recovery mode on the bricked n3DS? It might still work. It will force you to update the console though, but your save games and stuff will work.
Use "A+R+L+Up(DPad)" button combination on the bricked n3DS while it powers on. Hit power button then quickly use that button combination. Safe mode might still work on the console. Performing a system update from there will restore the missing titles and the console will boot again. You won't be able to use it with Gateway anymore.
You might be able to system transfer it over to the other n3DS. You'll have to find a way of using the eShop spoof on a 9.5 emunand on the new n3DS. I don't think the system transfer protocol changed from 9.5 and 9.8 (currently, you can't update emunand to anything past 9.5 on n3DS due to new Arm9 encryption keys)
I think for the n3DS, there's a NTR 2.0 plugin that spoofs eShop/NIM so you can use eShop/System Transfer. Make sure you are doing this on emunand of coarse. 9.2 sysnand probably isn't compatible with 9.8 system transfer.
n3DS won't let you system transfer to an o3DS by the way.
EDIT2: Nevermind saw your first post you mentioned you already tried this.
I looked up the title id and it appears to be "GPIO system-module" that he accidentally uninstalled.
I looked it up and Safe_Mode has it's own version that is a different title ID, So I find it odd that safe mode isn't working for you.