It's completely up to you, but my preference (strictly look-wise, haven't sat in those performance seats) is for the stock seats. They certainly look cool, but I would imagine you can get $3500+ for your VF kit, so that means you're paying $5500+ for seats? No thanks, but it is your car
Is the kit off of your car btw? Have you tried the BMS downpipe fix? They stopped selling it recently, but now that I think about it, it might fix your inspection issue. I have one not installed and would be willing to lend it to you for experimentation purposes (plan on using it once I get primary cat delete). How about contacting Bren tuning? I talked to one of his reps at a show and Bren personally owns an m3, so I think he can code the car so it passes inspection.