I think you should proceed like this:
Create an emuNAND, update that to 10.3 preferably running rxTools.
Now Smash runs again on that with save, updates and dlcs and as you didn't format your system and installed tickets to your purchases remain on the device, just make a backup prior to this of the content of your sd card, as it will be wiped if you use GW menu to format emuNAND, you should use the
emuNAND9Tool from d0k3 as you can take a different sd card than the one that is inserted if you want to do that, copy all contents over afterwards to keep all installed titles to that card.
Now you should create the xorpad with
decrypt9 that you are able to decrypt the FAT16 partition of any sysNAND or emiuNAND backup you create.
This is the risky part:
Follow this
guide, but use sysNAND instead (Backup sysNAND using gw menu, use
d0k3's tool for xoring and restoring the partition, modify the extracted fat16 partition with this
tool) to unlink your sysNAND from emuNAND without connecting to nintendo as it would wipe your purchases, you might need to do a bit of research to understand the applications and terms used.
If you do everything right you formatted your sysNAND to be able to use themehax to autoboot into the emuNAND, but if you unlikely screw up you may brick your 3DS if you delete the wrong file or restore the modified sysNAND backup incorrectly with gw menu, (always make a sysNAND backup for all cases with GW menu prior to restoring anything).
Themehax installation is a no brainer so I guess that needs no explanation.
That's it, anything can be used on your autobooted emuNAND after this that is as comfortable as using sysNAND, except gba vc or dsiware saves as they in the end boot from sysnand, even though only dsiware needs to be installed on both emuNAND and sysNAND to boot from emuNAND, the save from sysNAND is used in this case and as you formatted it you don't have one there and there's no tool until this date that extracts them as far as I know.
Hope I could help.