I don't know if this is any help or not, , , I trunk mounted my battery as well, I'm using an alternator that has been sitting since 1992 , a regulator that is the same, a starter , the same , and have no problems with charging. I would try another voltage regulator or take a voltage reading at the battery first and work my way back to the alternator . Could be a bad battery, or any of the affore mentioned !
Wish I could be more help !