Yes. Use .040" to 0.050" with those high-output coils. The size of gap can affect the idle performance: let that be your guide.
I had never thought about the increased gap affecting the idle, but it makes sense. On my K1 with Dyna 5ohm coils and Dyna-S I have the gaps set to 0.032". Do you think that's negatively affecting the idle?
Those 5-ohm Dyna coils make a little more voltage than the Honda coils, but at shorter duration. So, use the same stock 0.028" gap on that setup.
It's the 3-ohm coils where the big difference comes in. They can make up to 35kV at 14vDC supply and with larger plug gaps (stock coils are about 7.5kV). But, they discharge about 30% shorter duration than the Honda coils, so the surface area that gets exposed to the fuel-air mix needs to be a little bigger if possible. Larger gaps are one way to improve things here. Adding higher plug cap resistance to the 3-ohm coils (10k ohms instead of the more usual 5k ohms) will also slow the discharge time down about 10-15%, making it spark "longer", effectively. This is a good thing...there's plenty of extra spark voltage available in these 3-ohm coils, largely wasted. The SOHC4 engines only really need about 5kV to run to about 8500 RPM, so long as the spark duration stays above 1.0mS (stock coils are about 1.5mS duration with 7.5K ohm plug caps, Dyna 3-ohm coils are about 0.9mS without any resistance in the plug caps).