Im in that 3 hour window before we head off to friends/family for nosh and booze which probably won't see me sober to Tuesday so I'll give it a go now.
The 997 was a big improvement internally over the 996 and feels much more modern and fresh inside. The 996 does look a little dated but in the same way still has an appeal I think though the 997 is without question a big step forward. Being a Gen2 996 means it will have a better interior than the Gen 1 996's which missed things like a glovebox! In terms of drive the general feel between a 996 and 997 isn't that different but you are comparing a Turbo v a non Turbo and probably 2WD v 4WD so there will be some differences.
Performance wise the Turbo is still the quicker car but the difference will not be as much as you might expect until you get into big numbers. If I remeber correctly the 996 Turbo was 420bhp, the S (simply with the factory X50 mod added as standard, which gives new bigger turbo's and bits) was 450bhp and being a Porsche everyone of those horses will be there to play with, non will have gone walkabouts or be 'in the region of' statistics if well maintained and working. The 997 C2S was in Gen 1 form 355bhp I think so you can see where the extra shove comes from. To me the turbo engine lacks the sharpness of the non turbo but for a turbo engine it's leagues ahead of most in the way it delivers it horses. Cross country the turbo is epic, like a GT-R with 100plus BHP less simply and is a very nice car to drive quickly.
If it were my money I would go with the 996 GT3 MK2 but then it isn't so I'd go with the 997 C2S of the 2 above as it's fresher to be in, I prefer non turbo engines and it is just newer and I think better for it. However, if you plan to go tweaking as is your way a Turbo S will give you the best foundations as the extra bits offered by the X50 modification mean you can I believe go to close to 600bhp without too much effort and cost. Running costs wise you go from 12K (or 2 year) services intervals (I think) with a 996 Turbo to 24K and (2 year) intervals with a 997 though anyone who run's it past 10K without a service is mad in my book. OPC's will offer fixed price servicing and I am sure this info is on the Porsche website. There are more things to go wrong with a 6 turbo but if all runs well I don't think the running costs will be that much different.
You need to drive both and see which one you prefer. Give Sutton OPC a call and arrange to meet with them and test both cars is my advice.