What i have found is that output is good with the headlight disconnected (12.6 - 13V at idle and between 14 and 15V at 5000 rpm).
With the headlight on the meter needle hardly moves from 12.6V regardless of rpm.
The clymer manual doesn't specify whether voltage is to be measured during "daytime" or "nightime" conditions.
Should my voltage output be the same for headlight on or off with only amperage differing??
A voltmeter on the battery says more about the battery charge/drain status than it does the charging system output. If you also know the system loads, then you can infer charging system capability.
At any given run condition, the charging system either supplies enough power to run all the loads on a bike or it doesn't.
Using 12.6 V for battery full condition, a higher than 12.6v reading means that the battery is stable at full charge. A higher reading than 12.6V means that the charging system is not only running the bike loads, but also charging the battery. The vregs job is make sure the battery doesn't exceed 14.5V as that is bad for the battery. If the battery on a running bike drops below 12.6V, this means that it is draining, such as when the charging system is putting out less than what he the bike requires in system loads, and the battery is supplying the difference need by the bike loads.
The headlight significantly changes the the bike's total load on the charging system/battery. Nether supplies a constant voltage or output power. The alternator varies its output with RPM. The depleting battery supplies diminished power as it drains.
Your first report indicates that your Vreg knows its job and does it fine when the headlight is off and the charging system can not only keep up but well overcome the bike's loading with the headlight off.
The second report that 12.6V is tops with the headlight on suggests that the bike loads 'only just' meet the charging system capacity with no reserve. (This summation assumes that your report is NOT an instantaneous reading but one in which trends (using time) are considered, as a battery is not useful if it allows wild output voltage swings is short time periods with standard loads.)
Since you have a new regulator and rectifier, I would look at the Black wire voltage at the Regulator with the headlight on, and compare it to the actual battery voltage.
If you have a digital meter, place one probe on Battery POS and the other probe on Vreg black. The reading would indicate the voltage lost between those two points. If the Vreg and alternator are deprived of full battery power, the alternator output will diminish below full rated output. The alternator is rated at 150W @5000 RPM provided it has a 12V input to the field coil. It will make less than rated power when fed less than 12V on the white wire input.
You mentioned you have a Vetter installed. Does it have running lights? What bulb numbers do they have? Higher wattage lights steal more from the charging system and direct it away from the battery. Same could be true for replacement rear running lights or Turn sigs.
Cheers,