https://github.com/Plailect/Guide/wiki
This guide will walk you through the process. Make sure to read it thoroughly before starting, so that you know exactly what order steps need to be taken. Luma3DS will cover the desire for GBA VC and DSiWare. As for the DS games, Luma3DS includes TWL_FIRM and AGB_FIRM patches that should allow the Gateway Blue Card to function properly as a DS Flashcart.
Since the owner of the 2DS is also a Gateway User and wishes to continue to make use of his Gateway Red Card, there's some extra information that you should read regarding the current state of using Gateway alongside A9LH. Essentially, the 2DS is going to have to have an EmuNAND partition in some manner, as GW doesn't launch from FW higher than 9.2. There are pretty much two different setups you can go with, depending on your choice of priorities. Here's a guide that I put together that discusses the subject a bit further.
http://gbatemp.net/threads/guide-how-to-use-gw-luma3ds-a9lh.424117/