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User interface of that program bites the big one, but the data file is a simple text file that can be edited with Notepad. I found it easiest to get the configuration how I wanted it even though it wouldn't let me enter the numbers correctly, then edit the data file directly by figuring out what number meant what. (Can't complain tho ... it's free.)
If your combustion cycle is not "conventional", this route might not work for you, because it's expecting a conventional 2-stroke or 4-stroke piston engine operating more or less on the Otto cycle.
I don't know the mass flow-rate per valve on my motorcycle engine. It could be calculated (approximately) based on intake air density, revs, estimated volumetric efficiency, etc., and like others have noted, the mass flow rate "out" has to be the same as the mass flow rate "in". Your calculation would be just as accurate as mine. This is my roadrace bike, and I'm limited by the rulebook for what's done to the engine, so it's pretty much stock, and it's irrelevant to me what the mass flow rate is. The engine runs, the carbs are jetted correctly, it makes normal power, and beyond that, "it is what it is". No point analyzing what the rules won't let me change anyway, so I've not bothered.
Conventional Otto-cycle exhaust systems depend strongly on the remaining pressure in the cylinder to force exhaust out the exhaust valves when they open, this is why the exhaust valves are always smaller than intake. If you're doing something out-of-the-box that changes this, standard analysis might not do what you want it to do.