look for the nails that hold the soffit and /or facia boards up. A good magnet might be helpful here. . .
if you have confidence that your builder was good with the level-square-plumb aspect of his/her trade, you can estimate the location of the rest of the rafter based on that data. (here in california, with a plethora of fly-by-night developers, earthquakes and houses built on loose fill, that might be misplaced confidence. . .)
Use a square (or measured 3-4-5 triangle), plumb bobs, a straight edge and a tight string (chalk line) to transfer the location of the facia/soffet nail locations to the top of the roof. . . a couple of tripods might be useful, too.
basically, thus: if you can locate 2 points on a line, you can use those to project the line off into space.
get a good helper and a ladder.
find row of nails on the soffit/facia. you may want to verify with the studfinder or a couple of small nails that you are on the center of the rafter. set one plumb-bob so that the bob settles on the center of said row. we'll call this one the datum, for lack of creativity.
align the square or triangle with the (presumeably reasonably square) edge of the roof, with one arm out across the first coupla rows of shingles. line the edge of that arm with the datum plum-bob tip. the other end/tip of that arm/triangle forms the second point on the line . . .so cheat however you have to to make sure it agrees with the best information you have on the subject rafter.
take (or have the helper take) another plumb-bob to the ridgeline, and use it as the new endpoint of your projected line, or 'target'. move the target until the tip of the arm of the square, the datum plumb-bob and the target plumb-bob all line up. Use the straight edge as a sighting aid if you must look from the ground. take your time, and do it right.
mark the places that the points of the plumb-bobs settle at. stretch your chalk line between those points, and off to the next rafter. slow, tedious, exacting, and probably at least partially inaccurate, but if the alternative is tearing up the shingles and decking. . .
the above advice is free, and is, of course, worth exactly what you paid for it. . .
good luck-
-Dan