I would guess that the stock manifold has more torque because of the smaller runners and higher volicities through the runners more than the fact is has an egr, just a guess though. This would increase torque but hurt the upper rpm range of torque and hp. ON the smaller diameter headers for more torque, you should also get more torque there too, since it should help due to the same good volicities at lower rpm's which should help lower rpm exhaust scavaging.
A friend of mine found is looking to do the same thing as you are with your motor, make a low rpm torque motor with good gas milage. He found some kind of strange edelbrock intake that was tuned specifically for the purpose of low rpm torque. I need to find out the name of the intake. It has small runners for volicity and some unusual dual plane setup. I will get back with you when I find out more about it. Edelbrock quit making the intake quit a while back though so they aren't available new anymore. He found the intake on e-bay.
Don C