Now is good.
I drilled the trim cable holes in mine during the construction of the HS before I riveted anything together. There isn't really anything to line up between the fuselage and the HS since the manual trim cable comes up through a lightening hole in the rear deck of the fuselage and goes through the front HS spar, through the HS and then exits the rear HS spar into the left elevator. There's plenty of flex in the cable and plenty of room back there to get the cable into a hole in the front spar almost any place you could possibly want to put it.
The only possible alignment issues would be between the HS and the elevator and the holes in mine (located per plans) were dead on. Even if the holes in the rear spar and the elevator were off a bit there's still some room for error so I'd go ahead and drill 'em.