Does anyone know of any good reference material related to the compressible fluid flow through the internal combustion engine? I have yet to find what I'm looking for.
You couldn't possibly mean something like Gordon Blair's book on 4-stroke engine simulation? Although from what little I know about engines most flow is treated as incompressible, with Mach numbers of .6 or less in the intake.
Also check out the books by Winterbone & Pearson on manifold design.
The flow is compressible, otherwise pressure wave action wouldn't be such an important feature of intake & exhaust design. And of course you can get choked flow in valves and in (artificial) restrictors.