So after all the advice that was offered, this it what happened. I started off marking the centers of the old rails. Then used a plasma to cut the flanges off the old rails. That was working really nice until I let the smoke out of the plasma cutter. Finished them off with the torch and ground the slag on the edges so the pattern would lay on the new rails nice and flat. The plan was to set the pattern on the new rail align the center marks, clamp and make metal shavings. Mag drills don't like to stick to anything that isn't nice and clean so on the first hole the annular spun out and burnt up. The plan then evolved to making a very light center mark using 3/4" and 5/8" drill bits through the template, then removing the template and center punching the marks. This plan made the mag drill pay off.
Old rail used for template
I started drilling using Unibore bits. These bits are not for drilling this type of steel as it turns out. They ran smooth, but the shavings would be thinner and thinner until they just stop cutting making a nice work hardened hole.
Work hardened hole when bit stopped drilling.
Not knowing if it was operator error on cutting pressure / feed rate, my brother bought me a new set of Unibore bits. I proceeded to make the record 13 holes and burnt the new set up. This is getting expensive! Took a shot on some cheaper Evolution bits and that paid off big. They are a number or two harder on Brinell scale. They are hard to keep in a sweet spot but just keep cutting. On the holes that spun out we ended up just drilling them with twist bits, these proved to be too much for the Evolutions. I was told that it is possible to heat them to red then spin the annular back through the started hole, but didn't want to risk the base of the mag drill.
The moment of truth!!! Would any of the holes line up. First rail, no problem.
2nd rail, no problems either! So far so good.