Would you think dyslexia is a possibility, based on what you've seen? Looking at the reading level/ comprehension gap, one possibility might be that he is not decoding in the usual way, but rather is using other strategies and compensatory mechanisms. These can get the job done, and in a kid with high verbal skills and a good memory, can get the job done surprisingly well. However, for most people, by-passing decoding is inefficient and exhausting, using up all the available cognitive resources: there's no automaticity. So it may mean they can read OR they can think about what they're reading, but they struggle to do both at the same time. Can you see if his comprehension is much better when he is read to, vs. than when he reads himself? That might help differentiate a bit whether the block is in his reading or elsewhere.
You mentioned a number of reading issues that have improved since the VT. Do you still see a lot of skipping small words, and replacing big ones with logical but incorrect alternatives? These are common habits for dyslexics too, who seem to be particularly challenged by those small meaningless words, and whenever possible would rather guess a larger one from context/ first letter than attempt to decode. Another check would be spelling, which tends to remain abysmal even in dyslexics who are excellent readers.
