I own a 996S (from new for nearly 4 years) and have test ridden then 998S bip. First of all there is some difference between the models people are talking about 996 bip, 996S, 998 bip & 998S. If you read the models in this order they SHOULD get better from left to right.
996 bip ~116bhp, 996S ~124bhp, 998 bip ~124 bhp (testatretta) & 998S ~132 bhp (testastretta)
Now with this in mind, testing a 996 bip with a 998S gives you a winder margin for sensing the improvement. The 996S/998 bip is more subtle. Apart from the engine, there's not much difference in the 996S/998 bip. I'm not sure if the 998 bip has 4 pad brembos because i did notice a marked improvement in the brakes on the 998S which has got the 4 pad brembos. Did the 998bip have a 45mm exhaust - the 996S has a 50mm throughout.
I do love my bike but i've made it my bike by adding so much to it and will probably never sell it. I have also had no probs with mine (I bought mine new from P&H
too )
So my choice for either of these models would be on condition, mileage, service history and price - whatever comes out best from these criteria then buy that.