Hi! I want to help, but I don't have the energy to recount EVERYTHING I did.
Take a look at the below two tutorials. Most of what I did came from there.
[Tutorial] From 9.2 (or any lower firmware) to CFW 4.5, without Gateway
[TUTORIAL] How to export/import Gateway Card1 .sav to eShop/3ds/3dz with SaveDataFiler
Go as far as you can yourself (either IRL, or just planning in your head) and then tell me if and where you get stuck, or if there's something you don't understand. I'll be happy to explain what I did from there.
Note: I have a second Old 3DS (In addition to the EU N3DS and the Old 3DS with my eShop and save games) that I used to install the CFW. I don't think this was necessary, but it was helpful to me as I didn't have to worry about losing my eShop games and/or saves in the installation process.
Edit: Also, be forewarned: had I known before starting how long it would take to transfer the save, I wouldn't have begun in the first place.
So I managed to follow your guidelines, CFW installed, bigbluemenu installed. Problem is I turned off the system and put the CFW SD Card in my PC and copied over the Filer folder with my eShop save and savedatafiler.cia then put the card back in my console and it never boots into CFW again. And before I added these files I could boot in CFW every single time. Any idea whats wrong?

