When I converted my '65, I marked a reference line in-line with the original pedal placement,or in line with the bolt that they swing from. With the original pedal set removed, measure the cut-out and mark a center line both horizontally and vertically on the tin (top of foot well). Then find the center, again horizontally and vertically on the dual cylinder box. (note - make sure the legs on the box are square, use a stick to hold them in place and for marking the vertical center line. You should be able to match the center index marks and pedal bolt on the new box with the reference marks you have made on the tin. I masked the tin with 2" masking tape to mark on, since the new box is larger than the original.
Other things I found: I couldn't find a blanking plate for the hole, so I had to make one. You will have to move the wiper motor about 2". The old grommets for the wiper motor will likely need to be replaced. If it's a dual line brake master and clutch, you will need a different proportioning valve. I ran some angle steel reinforcement under the new box to keep it from flexing, and to add mounting support for the bolts. A dremal tool with a fiberglass cutting wheel works great for cutting out the sheet metal.
Luck on your project, Ron