I do hope someone makes an updated one including DeadSkullzJr‘s update
If you simply want to merge them, there are probably some programs or libraries for that. Afaik 'r4cce' allows you to import one cheatdb into another, although it won't resolve duplicates automatically.
But you can try this thing:
https://shocoman.github.io/Simple UsrcheatDB Editor/ . Some months ago I had a stupid idea to make a simple web analogue to r4cce to quickly edit cheats. It's super laggy, buggy, raw and unreliable but seems to be working fine with DeadSkullzJr's database (at least for now). In the top right corner press "Open UsrcheatDB" and point to DeadSkullzJr's usrcheat.dat file, then press "Merge with another UsrcheatDB" and select my cheat database (it's inside the file "all_patches_combined_in_one_usrcheat_db.zip" attached in the original post), and finally push the button "Download". It will merge games if they have identical game code and checksum. Again, not sure if it will work, I usually don't test things properly.
I can get c-stick aiming in Metroid Prime Hunters, but gyro isn't working. ZL + d-pad directions just move me. Is there something I need to do to enable? TWPatch has an option for unmapping the circle pad from the d-pad, but that doesn't sound like it would do what I need.
Just in case, you need to first press ZL and then (while still holding ZL) press DPad Down. Then it should work, or maybe you got the wrong cheat for another version?
Is it possible to swap the aiming to the circle pad and movement to the c-stick as in left-handed stylus mode?
Sort of, here is a version with swapped CPad and CStick if that's what you want.
How would the patch interact with the generic remapping tool in the main post? I ideally want to map jump to a shoulder button (and I guess boost and sniper zoom to another button) and maybe switch L&R with ZL&ZR (I have a grip that makes them bigger and lined up underneath rather than further inside).
It should work fine with my generic remapping tool, except for two things:
1) While using it with this game, you should unmap CPad from DPad there (that's what my mod expects and does, but the remapper can overwrite it)
2) You can't unmap ZL and ZR. The remapping is done via Nintendo's hardware register that knows nothing about anything non-NDS. You can map things to ZL or ZR, but not vice versa. In my mod these two buttons are sort of hardcoded to their respective functionality.
Do I need to use TWLmenu or could I use the cheat with my DSTwo to allow me to use save states?
You don't need TWLMenu. There just has to be a way to run cheatcodes (and TWPatcher has to be used, obviously). Don't know anything about DSTwo or other cards, but as I heard, these mods do work with them (or some of them)