Welcome Paul.
The 996R isn't quite the same engine as the 998s - there's a bit more exotica inside it so it will spin up quicker and make a bit more power (I think).
Chassis wise I don't think there's too much difference. Obviously you get the carbon panels, airbox etc ... with the R.
Of the bikes you've listed I'd have the 996R all day! But ... have you considered a 998R? I have one of these and it is the second generation testastretta engine and is very very tasty indeed
Seeing as you're new in town you'll need to find your way to the virtual bar and while you're there I'll be having a strong latte - cheers.