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As a general rule of thumb, the E46 has a better suspension than the E36 (330 vs 325/328). The 328 has more torque (but basically same bhp) than the 325 but it's OBD2 and has a more restrictive intake manifold.
As for coupe vs sedan, I've always been told that it makes no difference in rigidity. It might be easier to get in/out of a coupe in the event of an accident though. Somebody correct me if I'm wrong, but I thought I once heard that the sedan has a steeper windshield angle... May or may not affect aerodynamics.
If you decide on E36, it would definitely be worth it to find a non-moonroof specimen if you can, because that would save you the trouble of having to weld the moonroof sheet metal after you remove the moonroof mechanism. I don't know if any E46's shipped without moonroofs.
Then there's the weight thing. I believe the 325 is the lightest of the bunch.
I'm still as green as a noob can get, but from what I've read, it's speculated that the 325 won't be a front runner.
I'm sure Marshall and other seasoned veterans can provide more input. [/b]