Graphical circuit simulator like Logisim
For a complex project such as this, you would be better to use an HDL like Verilog or VHDL and a simulator.  

There are open source Verilog tools available like Icarus. Also since all the major FPGA vendors have a free version of their dev tools, you could just download and use these.
For example the free version of Xilinx ISE has HDL and schematic entry capabilites, an excellent simulation tool. Actel's (now Microsemi) Libero IDE comes with similar HDL/schematic entry and Modelsim for simulation.