I think the Eddy heads are another step above the GT40s, so you would definitely be picking up more performance as well as something that would work well if you were to add more performance options in the future (i.e. cam, manifold, carb, etc.). The GT40s are pretty good and would benefit from all of that too, just not as well as the Eddy heads. BUT, the GT40s, if you can find them easily in your selected yard, will probably be the best bang for your buck. I'm gonna guess you can get them for <$300 a set whereas the Eddy head, or pretty much any aftermarket head for that matter, will probably run you around $1k/set. And, since you already have the springs and know how to set them, replacing the seals and springs on the GT40s would be an at-home job. The only thing you'd probably want to do is double check the guide clearances and make sure the valves aren't sloppy like your heads are, maybe lap the valves, throw your new components on them and go. The upside would be you'd be into them for roughly $500 vs the +/-$1000 for the Eddys. A con could be that you may still have to send them to a shop to have new guides installed. As for the Eddys, chances are pretty good that you could order them and basically just throw them on the car. Most everything should be good, but I'd double check everything anyway. You never know who threw the components together, but Edelbrock should have a reputation to uphold, so they should stand behind their product.
I guess what I'm trying to say, in my long winded way, is that either choice would be good as your engine sits now. The choice is yours as to how far you want to go with it all.
Now, if you decide to go with aftermarket, there are a plethora of options; some more expensive, some less. One example off the top of my head would be Speedway Motor's Flo-Tek heads:
You don't need to spend a fortune to get a top-performing, lightweight aluminum cylinder head for your small-block Ford V8. This Flo-Tek head has a long list of high-end features, minus the hefty price tag. Will likely need to plug the EGR connection holes in the end of these heads on 86-up...
www.speedwaymotors.com
They were compared to other offerings and did fairly well as Hot Rod tested and published:
We go hands on as we bolt-on six budget Ford heads onto our Ford Racing Boss 302 crate engine to see which is the best bang for your buck. The results might surprise you so see it for yourself in the February 2013 issue of Car Craft Magazine. six budget ford heads that work
www.hotrod.com
There are SO many options! Of course, it all depends on how far you wanna go and how much $$$ you wanna spend....