A fully charged battery, after resting for two hours, reads about 12.6V with no load on it.
A depleted battery, being charged, can read 13.5v on the way to the peak charge voltage of 14.5.
Once the battery reads 14.5 v, the regulator turns down the alternator output to prevent overcharging the battery.
The regulator cycles the alternator on and off rapidly. And, it is not unusual to average 13.8 V.
The type of meter can make a difference in readings too. If you have a peak hold function what does that read? If it is an averaging meter, what is it's sample rate?
The Halogen headlight, if larger wattage than the 40/50 that was stock, will make it more difficult for the alternator to peak charge the battery.
The shop manual assumes you have stock equipment on the bike.
Again I ask. What problems are you having with the bike?