I have the same printer, with the same problems with the Cartridges/chips, and also with the QTR.
For the QTR I fixed as:
Go to the folder: /Applications/QuadToneRIP/Profiles/3800-3880-K7
Rename the install script from Install3880-K7.command to Install3885-K7=3880.command
The idea is to create a printer called Quad3885-K7 but use the 3880 driver.
Just be careful to get the name exact -- no spaces or other characters.
Then you can run the script for your printer and setup.
I hope with the carts we have a solution, otherwise I guess we will need to buy a new ones?