OK its late and i will ramble on here.............
Break in of a modern engine, especially bike engines with much tighter tolerances than the average A-series might well be different. I know that most guys who race cars that are not registered, don't take it very easy when they first rebuild an engine. If the report was in a paper by a recognised metrology engineer, published in a recognised engineering journal it would have more credibility than a website and the is this true or not argument would not ensue......no offence to anyone here of course
as for the smaller port theory, all engine design is a compromise. If you have a certain rev range, and a certain volumetric efficiency, and a certain intake runner length, then at a particular point you might get more power from a smaller port. This is the case if you have a long inlet runner, and low revs. A smaller port will maintain the intake gas velocity such that the piston has to do less sucking to fill. think of the exhaust extractor theory in reverse

But at some point as the revs rise and the volume of air demanded by the engine increases, that port just ain't gunna flow enough air so has to be enlarged. Classic example is the old T-VIS dual inlet runner system on toyota 4AGE engines. Do a google search, i'm too tired to explain how it works

Suffice to say that when the butterflies are removed from teh T-VIS the dual inlet runners are just too big to maintain velocity at low revs and drivability goes out the window. When toyota ditched the T-VIS system for a single compromised length inlet runner, they reduced the inle port size and changed its shape to round instead of oval. To be honest, dyno results for race engines with the different ports show bugger all difference at the 6-7k rev area.
polishing is a bling thing really IMO. depending on the combustion chamber shape and the efficiency of the mixing of the fuel, it can actually be of benefit to have inlet ports with a helix cut into them to promote swirl. I have read elsewhere that it marginally helps with exhaust flow, but we are talking boundary layer stuff if the flow is subsonic. if the exhaust gas reaches near sonic velocities it may be of benefit to remove anything that will induce a shock wave, since that will kill the flow dramatically. Anyone know what speed and pressure the exhaust gas is at in a-series? Speed of sound is approx 300m/s at sea level in a standard atmosphere, and will be much lower at higher pressure.
The flowbench does not represent the variation in piston and gas velocity throughout the stroke, which when combined with the valve lift and the shape of everything in on the way, determines the actual fill of the cylinder. Plus the combustion chamber shape is a big factor that determines the efficiency of the burn. But the flow bench is a great standard measurement device that allows things to be compared with a degree of confidence.
There is only one way to increase the output from an engine, and that is to increase the mass flow of gas processed (done the maths from first principles, got the degree, not boasting really

). How you do that is up to you, since increasing revs, reducing inlet and exhaust restrictions, increasing cam duration, turbo or supercharging, or even simply increasing the density of the inlet charge (by cooling

) will increase the mass flow.
my $.02
michael
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