Okay, Plugging your numbers into BeerSmith I get 1.066 pre-boil.
Link to recipe I through together So you were pretty close but something was off and I agree you may need to change something like a longer sparge. But most importantly, a 90 min boil is going to require more wort than a 60 min boil. In this case BS suggests almost 8.5 gallons in your boil kettle. I typically boil off 1.5-2 gallons in a 60 min boil. You only boiled off 1 gallon in 90 min which should have been closer to 3 gallons. So, your boil could not have been very vigorous. Also, BS puts this at 1.099 into the fermenter. Which you were way off of. If you had 8.5 gallons pre-boil, at a gravity of 1.055 it would have helped you to get to the 1.099 having the extra 2 gallons to boil off. Even @1.055, you could have boiled down to 5 gallons and made it into the 1.090's.
Also, I think you have a few numbers wrong or your hydrometer is off but 6.5 gallons @ 1.055 equals 357.5 gravity units. If you boil off 1 gallon and divide that into the 5 gallons left it's only a gravity of 1.071 not 1.082 post boil as you have stated. so something is not right.
Does this make sense?