You're not going to be able to get around that fillet thing unless you build it into the sketch. You'll have to manually click on every corner. There's not a universal fillet all corners AFAIK.
I believe you can get the pattern tool to follow a series of points. Try laying out each row with a point indicating a corner or center of the hole sketch. Then use the pattern tool to pattern it along those points.
If I were to sketch the columns and rows, I'd figure out the center points and draw points and construction lines.
But you can also ask jdcarpe and swill how they got their setups to work out. That's just how I would do it.