* Update *
I thought long and hard about this and decided to simply sand down the one brake line spot on the new master cylinder since it was only like 1.5mm too deep, I protected the port with a small square of black tape and pressed in a chunk of "Dap Blue Stik Reusable Adhesive Putty", then I put it in the vice and used my "MAX XR Oscillating Multi-Tool" to slowly sand it down, I thought about using a grinder but i would think that would have melted the aluminum and destroyed the threads, sanding like this worked perfectly and didn't harm the threads at all, gently blew out the bits of metal with the air compressor, pulled out the Dap and tape, tested the line and it fit great, I figured since the bolt on the line didnt seat on the cylinder anyway because it seats on the compression fitting inside that I would be safe so i sanded to like 2mm, problem solved, re bench bled it and its good to go.