When facing educational assessments for IEPs, what tests actually help determine what will help guide goals and services for Middle School kids with Hyperlexia? Our son is not great at standardized tests, so these are not a great source of present levels or even cognitive functioning?!

What schools use are normed assessments.  These are tests that a large cross section of children have answered and based on your child's score, they can determine where they are on the bell curve for the skill being tested.  Standardized tests are not normed.  They are supposed to be a measure of how well a student has met the state standards for a subject.  If they do this, why did my son pass the algebra standardized test for my state and fail algebra?  I believe things played out this way because the test didn't work.

With your son, I'd want his reading and listening comprehension tested.  I'd expect he does OK with listening but not with reading comprehension.