13.8 is perfectly normal for a voltage reading across the battery terminals if the battery is in good shape. The alternator wont need to raise the voltage via the field coil if the battery is healthy. A fully charged battery reads 12.4 to 12.7 when sitting on the bench. If the battery is new, the charging system wont bump it up hardly at all, especially if theres no current draw.
When the engine is running, pull on the headlights and switch on some accessories, see if the voltage increases. If it does, the alternator is charging properly.
I would bet on a bad cable connection at the starter terminal now that you say you had the plenum off and was under there dinkin' around....or a bad battery cable connection either at the + or - terminal. Also check the 12V feed wire on the back of the alternator and see if its tight as well as the purple wire to the starter itself.