Hmm, my answer is closest to #4, with a bit of 3 and 6 thrown in.
Let's use parentheses to clarify the meaning of your examples:
In good years, the patchwork (of green fields [that surround the San Joaquin Valley town]) bustles with farm workers, many of them in the area just for the season.
(By the way, I think this is a flawed problem, and not worthy of all the attention it gets on the forums.)
In an effort improve the quality of patient care, Dr. Lydia Temoscho is directing one (of several clinical research projects that seek to determine how helpful psychological counseling is in supplementing the medical treatment of serious disease).
The use of lie detectors is based on the assumption that lying produces emotional reactions (in an individual) that, in turn, create unconscious physiological responses. (I added a plural here; otherwise, you'd need to add "an" before "unconscious.")
. . . a patent for one (of Kirchoff's laws), an observation
So, in short, when you see a modifier following a prepositional phrase, there is no concrete rule saying whether the modifier applies to the original noun or to the object of the prepositional phrase. You need to use meaning to make the determination. As you said in #3, you may also use the following verb (among other clues) to help you decide. Here are a few more examples off the top of my head (all correct):
Police have captured one of a ring of drug smugglers who have been plaguing the area. (smugglers who)
Members of the committee who do not wish to vote may leave early. (Members . . . who)
The extensive network of caverns that lie beneath the city has yet to be thoroughly explored. (network . . . has yet, caverns that lie)
The price of steel, which had fluctuated wildly for many years, began a steady decline after the labor dispute. (price . . . which)
Notice that there isn't much ambiguity here. In each case, only one reading makes sense. You might make a case for "network (of caverns) that lies," but that's about it. If there is more than one valid way to read the sentence, there will probably be another split that makes the answer clear, or one of the choices will be a distinct departure from the intended meaning conveyed by the other choices.
I hope that helps. Dig up more examples for Supreme Court consideration if you like . . .
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