I purchased a primary residence in 2005 for $269k, converted to rental in 2013 with $170k fmv, and sold in 2016 for $225k. Did I really just realize a gain of $55k?

No, you don't have any gain or loss.

TurboTax is not set up to properly guide you for this (it would make you pay taxes on $55,000).  This answer may help you report it:

https://ttlc.intuit.com/questions/2936029-sale-of-rental-property?jump_to=answer_4870589

You are my savior. I've been working on that for days not understanding how one clause puts me at a loss, but the lesser of them somehow puts me at a gain. Having neither gain or loss makes sense, splitting the difference. Thank you for your prompt response!