here's a question for the original poster -
how accurately can you get a flame cut hole in the piece? from what you said i assume that you have to put the hole in after the two 1" plates are welded to the web of the w12x87, correct? this makes the flame cutting operation more difficult than if you were cutting the holes in each piece then weldign them together. it also sounds like you are in a fairly remote area, and i don't know what is available for services, but would this be any easier to do, and can you get modifications approved:
flame cut a larger hole (+/-5") and weld in a sleeve where the pin goes. assuming you can source suitable round stock i would think it might be easier to find a local that has the capability to chuck up and drill/bore a 3" hole through short lengths of round stock. you could then weld these in to the flame cut hole you created. this isn't extremely easy or cheap, but trying to use a boring head on a mag drill to do these repeatedly sounds pretty tedious and also not cheap. i also have no clue how your approval process works, such as whether you can even get changes like this approved, or how long the approval process takes, and whether that blows your schedule out the window.