The credit guidelines for USDA and FHA loans aren't that different, but USDA loans do have an income limit which you may exceed, so you'll want to look into that. You can check both property eligibility and income limits on the USDA website:
Also, the FHA loan problem you're having may be more of the lender your working with. I would take that appraisal and show it to multiple FHA lenders in your area. If they would accept those comparative sales, you may be fine.
The rental income comparison may be the hardest part. You need to have enough money down to where the estimated rental income x the lenders acceptable occupancy rate is enough to cover all the units. You can read a little more on the topic on my blog post here: