So the biggest headache has been setting up the N3DS compared to the O3DS which was pretty straight forward and your fuck up's would lead to new discoveries.
Before I start, It's always good practice to ALWAYS have a backup of your 9.2 EmuNAND with EmuNANDTool. However to backup you need to use 1.0.3 and to inject it back you need to use this 1.0.1 as injecting a NAND backup via 1.0.3 will return an invalid NAND size error.
If you're getting a black screen after updating to RX 9.5, or the infamous "Setting up Home Menu" to black screen. Then one solution is plugging in your SD Card to the PC > Nintendo 3DS folder > Identify your EmuNAND's profile, then back up and delete it from the SD Card (However doing so would render the EmuNAND without a way to install FBI, but fret not)
Boot into EmuNAND, This time, it will work 100%. Let it create the default profile, home menu and thememenu. Once that's done, power down and take out the SDCard. There will be a folder called 0000008f under extdata/00000000 that will be added compared to your initial backup. Now copy that folder, and place it into your backed up version of your EmuNAND's profile under extdata/00000000
Now copy the complete profile and paste it back into your SD Card>Nintendo 3DS folder replacing any files it asks you to replace.
*Boot up your N3DS into RX 9.5, this time it will load, and have all the CIA's installed via PastaCFW along with FBI.
Massive thanks to
@Ryccardo for dealing with my silliness.