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Take a deep breathe! We had the same issue and wasn't able to get approved for a USDA guaranteed loan but we just got our first set of (easy) conditions from the underwriter for a FHA loan.
My husband and I both have student loans. Mine are on an income-based repayment plan and I pay $225 a month. My husband's loans are in deferrment until 2019 because he is in school. I was told that as long as his loans are defered for 12 months after the closing date, they will not be included in the debt ratio for FHA loans... the 1% comes into play for USDA and conventional mortgagess. I was also told that USDA counts 1% of deferred payments as well. The reasoning is that IBR payments changed yearly.
It is also rumored that FHA may be changing the way it counts income based repayment student loans in the very near future.
I'm no expert but this is my limited knowledge on the topic since we were denied one loan type because of the infamous student loans.
Good luck.