All the areas where you currently need to manually change cicoparser, Dune does everywhere. It jumps based on flags, makes indirect jumps and calls (Dune dynamically loads in video, pcm audio and midi drivers), it jumps wildly around, into, and out of the middle of other procedures, and so on. I'd love to see you try, though.
Secondly, I don't really see a great advantage of cicoparser over emulating the CPU. You've converted the disassembled code to assembler-in-C, but you haven't reverse engineered the application. If I've successfully converted an application with cicoparser, yes, I can run it, but I haven't learned much about how the original application works. It can be a good starting point for reverse engineering though.
We had an engine in ScummVM that was created with a similar process. The application was organized well enough (with clear function boundaries, etc.) that the engine could gradually be transitioned to proper C.