Yes, every EP I'm aware of goes off the model. You might go to the EP4 thread anyway to see if there is an easy way to fix this, as you will like EP anyway.
Anyway, I just made sure it will work with meta pricing and it did on this product on a secondary site:
http://www.promdressesforless.us/alyce-6116-p-344.html
Price is in the title in view source. Rest of products are set to "0", as normal for me.
Back to your issue, looks like you'll be spending a couple of hours in admin. While your at it with the meta price, maybe you should add model nos. for Easy Populate. To make it easier, we usually use the same as the product name, not sure how that'll work for you. And characters are limited in number, unless change it (as I recall, in db.)
Just note that all model numbers have to be unique...no duplicates.