Adam, I believe you are exactly right! The .001" tolerance you mentioned is for a brand new block/bore/crankcase! And yes, the greatest wear will usually be in the port area due to minimal sleeve support. Your measurements seem like normal wear for an engine of that age, and I’m sure it will run just fine.
I will look in my old Evinrude manual to see if it mentions acceptable bore/out of round tolerances, which manual are you using?