A system simulator that allows for verilog modifications?
I highly doubt any simulator goes anywhere near that low level. All simulators like QEMU do is translate instructions from a virtual environment to be run on the host processor. If you are "emulating" (I use that term loosely) one architecture on another (e.g. one of the many ARM sets on an i386), the simulator doesn't care about how an ARM processor would execute, it only cares what the expected result from each instruction might be.

Processors do a lot to get the intended result from each instruction, and modern processors have complexity in terms of instruction pipelines, branch prediction, caching, parallel processing, and so on. None of these are necessary to get the intended result in a simulator as they are designed for performance.

Nobody would invest the time (especially for free software) to design for example an x86 processor from scratch in Verilog and then run simulations at the hardware level. Aside from anything such a simulation would take an eternity to run - mere nanoseconds would take minutes to simulate.