Looking at this recipe I don't see any reason why you couldn't use puff pastry as the container.
The only ways that the preparation would be different is:
puff pastry doesn't dry out as fast as filo so you don't have to worry about the wet towel in the instructions.
You wouldn't want to do multiple layers of puff pastry as the recipe calls for. You would just form a single pouch to hold your filling and seal it well.
Know that the texture will be different of course. The filo will be a bit more crisp and the layers larger and more distinct- filo is also a lot more work. You may find that the baking time needs to be adjusted a little but I don't think it will be very different if at all. Cook them until they're golden using the recipe's time as a starting point.
This recipe is in a Mediterranean style and filo would be more traditional but puff pastry would produce something tasty.
Puff pastry is a laminated dough, with very strong gluten development, so an extra couple of days in the refrigerator should not have caused problems.
450 F seems like a typical temperature, and the time seems in the normal range.
The only thing you have mentioned is that is definitely outside the standard treatment is trimming the edges with a butter knife. Normally, you want to trim or cut puff pastry with a very sharp knife or pizza cutter, in order to cleanly cut through the layers. A blunt knife like a butter knife can mash the layers together, making it hard for them to separate at the edges of the pastry.
Still, this should have lead to lopsided or strangely risen pastry, rather than a complete failure to rise, especially in the center.
The other possibility is that the dough was too warm when you rolled and worked it, or that you rolled it too much, which would work the fat or butter layers into the dough phase, rather than keeping discrete layers of flour then fat, which is what allows the rise.
Best Answer
A few points to consider...
Try docking the pastry.
ref: http://powerhungry.com/2009/02/puff-pastry-docking/
In general, to cook food more evenly, one should cook longer at a lower temperature. The problem is that the dough on the bottom of your crust is not reaching a high enough temperature by the time the top of your crust is done cooking.
Puff Pastry is notoriously finicky. Be sure to handle the dough according to puff pastry best practices to ensure the layers do not collapse and stick together.
Pepperidge Farm has a tutorial website (http://www.puffpastry.com/videos-and-tips#howto-demos) to help people with puff pastry issues, but it doesn't appear to cover much detail.