I was going to reply to a 650 post with this but didin't want to add any confusion. After I wrote it all, I thought the 650 may be different (electronic ignition). Maybe I'll research it. Here's what I was thinking:
I will contend that it makes no difference if the camshaft is 180 out (on these Honda fours) or not. Here’s why: We know the 4 cycle engine consists of a compression, power, exhaust, and intake cycle. From taking enough of these engines apart, I know that cylinders 1/4 are 180 degrees apart from 2/3. So if 1/4 are on an intake cycle, 2/3 are on exhaust. The layout is thus:
1/4 C -> P -> E -> I
2/3 I -> C -> P ->E
If you rotate the camshaft exactly 180 degrees, you simply flip what 1/4 was doing with what 2/3 was doing. There would be no colliding of pistons and valves. But how would the ignition timing work then? Wouldn’t the plugs be trying to fire at the top of the exhaust stroke? Yes, they would and they do anyway. These are wasted spark ignitions. The camshaft turns 1/2 turn for every revolution of the crankshaft. Therefore, the 1/4 "F" and 2/3 "F" timing marks are hit twice per each revolution of the camshaft and are 180 degrees apart. Depending on the position of the camshaft, the “wasted” spark could be the “effective” spark or vice versa.
Based on my own personal observations... When I was putting my 550 top end together, the manual I have stated to “line up slot in the camshaft with the top of the cylinder head.” But it did not say which way the slot should be pointing (toward the front or toward the back of the motor). After some thought, I went back and looked at the manual and there was a photo that showed the slot toward the front. I took my top end apart and shifted mine 180 degrees (I did slot to back). It had no effect.