of course there's a difference, thats why they offer both models.
mainly its the 2 door vs. 4 door debate that you have to go over with yourself and your family.
then its the styling, coupe's always have nicer arches than sedans.
the coupe has a sportier suspension and exhaust note
both use the same engine and transmission.

As far as 5AT vs. 6MT, you have to decide between what you need, and what you want

<font color=green>-Rambo</font color=green>
G35c 6MT DG/Willow

 

Well, Rambo's given you a lot of it, I'll try to finish things off:
The sedan is quoted at having 260 hp to the Coupe's 280 - but the Coupe is supposedly a bit heavier.

Numbers wise, the Coupe IS faster, there's no arguing that, and the 6MT is faster than the auto (given a good driver, of course). Theoretically, a coupe should walk a sedan no matter what, but a good driver in a 6MT sedan should be able to hold his own against an auto Coupe except in the twisties - there, the suspension upgrades will give a significant advantage to the Coupe.

Other differences are almost too numerous to mention - but one notable difference is the availability of Brembo brakes and 18" rolling stock on the Coupes, not available on the sedan (Limited slip differential possibly also, not sure if that's available on the sedan).

Best bet is go to http://www.infiniti.com and check out the specs on each, and then maybe visit http://www.motortrend.com and look up the Car Of The Year articles (look hard enough, you'll find the entire published article on the G35's there), that'll give you a lot of road tested specs on their performance.

2003 G35 Coupe 6MT Leather
Premium, Aero
"There is no spoon"

 

On a straight away the 6mt sedan should get the 6mt coupe though... Even though one has 280 and the other has 260 at Stillen Day they were both Dynoing at the same amount of HP to the wheels which is most important... The Sedan is 200lbs lighter then the coupe giving it advantage... Oh yea a few reps at Stillen Day said the Sedan is easier to tune since the Coupe is already well tuned...

I own a 5AT coupe because it looked nice and don't have a need for 4 doors...I also drive in bumper to bumper traffic everyday on the freeway... I'm single also....

 

I was told that the coupe and the sport suspension in the sedans are identical. And based on several ride and drives in the coupe I have every reason to believe that's accurate. However when the coupe get's to take advantage of it's LSD, the sedans game is finished. I'll also wage money that the sedan has a higher center of gravity, least IMO.

Ivry 6mt sed
Injen CAI, 22" resonator
8X18 Enkei RPM2 45mm
Kumho MX 245/40
clear corners