The fact that your son has CAPD shouldn't make taking a 45-minute test hard for him. However, the CAPD may have affected his ability to process language so that he hasn't learned how to read well enough to do well on the test. You said, "the focus and attention just isn't there." This is another matter. He may have difficulty with auditory attention in class (clearly related to the CAPD), and his ability to sustain his focus on a task may have to do with how difficult the test is.
An important issue is whether your son still requires the modifications that the school wants to take away in order to be successful on such a test. The teachers say that he is struggling with directions and comprehension, but are these problems so severe that he can't handle the demands of this test? If you and teachers aren't sure, then I would suggest having him take a trial test to see how he might fare in the actual test situation. If he does ok, count your blessings and be optimistic that he'll also do well on the "real" test.