Do not use flaked rye. It should be mashed. This is an extract beer and you have no enzymes from base malt so all that will be contributed by the rye will be starch that will affect the overall quality of your beer and be ignored by the yeast.
Also, you did not adjust the default hopville boil/batch specs... are you doing a 4 gallon boil then topping off with 2 gallons of water with 1 gallon of expected evaporation? I highly recommend a full volume boil with no top off water for an IPA.
For a 5 gallon IPA, you want about 5-7 oz. of total hops - 3 oz. won't cut it.
I like to bitter with 1/2 oz. then give another 1/2 oz. charge around 30/20... then blast it late at anywhere from 15-10-5-0 with the rest of my hops and use AT LEAST a 0.50 oz. dryhops PER gallon of beer.