...getting rid of the center "clunk",
Better way to achieve a clean center is a CAM and follower gimbal. Why this system is used by VKB, VirPil, Slaw, MFG, BRD.
Anyway, this guy achieve a good result using a motorcycle U-join:https://www.youtube.com/watch?v=-JNjoF49p5o
The electronics part is simple and easy.
1 - Is there a means of using some sort of "adaptor" between the hall effects outputs and the factory CH controller?
Hall sensor like in the linked YT video (Allegro a1324LUAT, Honeywell SS495A1, SCE H49A...) work in analog mode - voltage variation, like an conventional potentiometer; so is just matter to replace the pot' with one, no extra electronic adapter is required. Just their pinout is different relative to an potentiometer, check datasheet.
The "difficult" part of DIY Hall assembly is tuning the position of the sensor in the center of magnetic field, since they are high sensitive. Require a bit of trials and patience.
With a Hall sensor in potentiomer format, this "tuning" is skip. Pay attention that you need a model with lower "effective electric angle" for match gimbal movement, the linked one is 60º model, an 35º is available.https://www.digikey.com/en/products/detail/tt-electronics-bi/6127V1A60L-5/2620660
2 - Or connect the hall effects axes to a separate Arduino controller running MMJoy (or something similar) while retaining the buttons/hat switches etc. still being run through the original CH controller. Doing this I don't know what DCS/IL2 would do with those two different inputs.
Yest, this is another option, some people already did this combination, using an new USB controller with more resolution for manage de axes and keep the (obsolete) original controller for buttons, what allow keep programming then with original software - who had "hiccups" in latest Windows 10 versions. Anyway Joystick Gremlin give similar functionality, without brand restriction.
This approach means two USB cables for each device and that they will be for Windows and games two controllers, neither DCS or Il-2GB care about the input source, since they allow use around 8-10 controllers or more.
3 - (IMO) Ideal is use a better USB controller, at least for axes, CH is an old 1999 tech with 8 bits (256) points or resolution only, and so just one USB cable for device. At least for rudder pedal
Arduino PRO Micro + MMJoy2 firmware or STM32F103 + FreeJoy firmware give you a 10 and 12 bits USB controller - costing ~$5, with configurable features (like axes response curve), support for advanced contact less sensors in digital model, like TLE5010/11
, support incremental encoders, buttons modes...
Both MMjoy2 or FreeJoy firmware allow you set the controller name like you want, as well VID/PID number, what allow, for example, that Windows see joy before throttle or vice versa.
As said, modern games - DCS, L-2:GB don't care about names and brands of controllers.
Neither MMjo2 or FreeJoy require custom drivers for install, both use Windows native HID drivers, so is "plug and play".
BTW - This joystick "overhauling" is fun.