Paul~
Sorry to see this damage! But, it looks like you've already got the repairs well in hand.
A couple of thoughts.
First, you should definitely have motor mount pads on the inside. (Of course, I cannot find them after a quick web search....) They both protect the transom (with rubber or leather pads inside) AND - most important - prevent the motor from twisting up an off the transom (I learned that lesson the hard way in my youth).
Rather than use aluminum on the outside, I would consider something softer - either 1/4" plywood (just painted - expect it to get chewed up a bit) or hard rubber. They used to make pads for this purpose - maybe still do. (see
http://www.aquamarineboat.com/index.php?mode=prod&id=243&PHPSESSID=a27cf437c0d456ee34ae93b1763eb869). I always keep some rubber around from truck inner tubes for purposes like this. You could just glue it on.
All the best,
SJS