Josh: You have to make a decision about the intake manifold. If you go with the stock 3.0 manifold, you cannot use the Contour EGR or the IMRC.
I'm using the 2.5 intake because the 3.0 throttle body is limited to 60mm. I already have a custom machined 62mm t-body and have a hybrid 65mm for my 3.0. The stock Taurus throttle body is very different from ours and you cannot swap. About all you can do is to optimize it.
You using SVT cams?
96 SE with '01 3.0. Custom 65mm throttle body, custom LIM, double honed SVT UIM, SVT cams, headers, custom Y pipe, custom mandrel bent SS 2.5" exhaust, Quaife, drivetrain torque brace and custom frt & rr suspension.
I make custom suspension parts.