Mark,
First, it is usually a good idea to contact Van's about any structural questions you may have. Van's folks definitely know best. Here, you can never be completely sure about the validity of the advice you get. Like the following, for example:
Structurally the -5 rivets should be fine as long as you were able to maintain adequate edge distances.
Also, something I learned from those that had gone before was when you have to drill out a rivet and you slightly enlarge the hole, you don't necessairly have to go up to the next size rivet. You can take a rivet of the same diameter that is .5 to 1 longer than the original rivet and "pre-squeeze" it a little. That will fatten the rivet up just a little so that it fits snug in the slightly larger hole. It is kind of like manufacturing your own -4.2 rivets.
I hope this helps. It is all a great learning experinece. Especially the emp kit.