IS your EGR system still fully functional? I've heard before that you can eliminate the coolant passages to the EGR spacer even if you still have a functioning EGR. Do something like that at your own risk though, I can't say I've done it myself.
If you DON'T have a functional EGR system, there is no reason to run coolant through the spacer at all.
Accufab stuff is supposed to be really high quality, I can't imagine how it would be warped. Are your gasket surfaces clear of scratches? Are you torquing to spec? Also, torque the bolts in the same fashion you would the lugs on your car, that might help you get a better seal.
I wonder if the boost you're running through the system with that S-Trim is having some effect.