Therefore, Do I prune now, or wait until after they bloom? Do I get aggressive and cut massive portions of limbs down, or spread it out over two seasons?
Secondly, I want to order more fruit trees and perhaps a filbert tree. Do you recomend a mail order company for these items? If so, whom?
Pruning isn't hard, but you should do it right to have the best effect on your trees. For rehabilitating a standard apple, you want to remove 1/3 of the branches a year so that over 3 years you restore the tree. You want to prune most fruit trees when they're dormant (peaches are an exception). Don't go at it with a chainsaw. Radical pruning can harm a tree. The goal of pruning is to stimulate the tree to fruit and to shape the tree so it is productive and easy to take fruit off of.
Check out Pruning Made Simple
by Lewis Hill for more information . It's worth owning this book because he explains how to properly prune fruit, nut, berry and even hedges.
You mentioned dead limbs etc. There is a particularly nasty apple disease is called Fire blight. [I had a link here to a site with good info on fireblight at the University of West Va, but because I'm a newbee the server made me take it out. Do a google search and you'll find it.]
It's a bacterial infection that's spread by bees during pollination. It makes the limbs of the trees look like they've been scorched by fire. If you see signs of it on the trunk of the tree, you should consider turning the tree into firewood.
If you don't get rid of diseased trees nearby, you risk infecting any new trees you put in.
Lastly, we've had really good luck buying from Miller Nurseries they're online at millernurseries.com. I live in upstate NY, so having stock from the fingerlakes area is good because it's even colder there than where we live.