About Spanner1's comment: you definitely will have meaningful resistance measurements on the hot leads to ground if you have an ohmmeter that reads accurately down to an ohm or so and a good set of test leads. You must zero the ohmmeter before the measurement by shorting the test leads and adjusting to zero to eliminate the resistance of your test leads and to compensate for the aging of the ohmmeter battery. Digital meters sometimes have this zero adjustment available internally. Otherwise your readings may all seem to be "short" with the meter going to zero.
I second his advice about checking the condition of the fuse holder carefully. Corrosion or poor contacts will cause heating and may melt the fuse. Melted or burned insulation on the back of the fuse holder will show you that this is happening. As well as being clean, they should also grip the fuse tightly for best contact. With the fuse out, you can bend the clips together slightly so that they grip the fuse better. Check that you are using the correct physical size fuses. The 3AG type common in North American are too long for the Honda fuse holder and don't make good contact with the clips. You should get the proper metric sized fuses from a Honda dealer - they are still available at reasonable cost.
I'd follow Mystic_1's advice.
Also, since you had it running without the fuse blowing for a time, you may have an intermittent short, for example, frayed insulation that allows wires to touch each other or the ground if, for example, you turn the front wheel with the handlebars. A careful inspection of the entire harness might be in order.