Well I'll admit I'm have a hard time articulating my thoughts....
But this is my last attempt....
Here's a picture of a 1970 Cuda I found on the Internet. It shows how much "roof" is seen from that angle. Now if you took a flat bar and ran it across the roof at it's center point from driver's side to passenger's side....Then measured the "visual" difference between that bar and the upper stainless trim of the windshield you will most likely get a greater number on your 4dr car. Also, if the 4dr car had drip rail moldings (a must for a vinyl roof car) those moldings would appear higher then the top of the windshield moldings.
I'm not critiquing the craftsmanship in the work done, I'm simply pointing out that the method of construction you've chosen has resulted in a raised roof appearance....I'm sure Chrysler would have had the same results using the same available assembly line parts.
It's unavoidable.
Critics would argue the car should be a 4dr hardtop, not a 4dr coupe in the first place, but obviously that would be more costly developing new "one off" side glass.
P.S.
Oh can you double check my spelling on my last few posts....my Google toolbar thing isn't working again today.