The engine is certainly fine past 100k miles. I got my 97 GT with 95k miles and have put in 30 passes at the track and taken it to 166k miles by now. The engine is still very strong and never smokes. In fact, my best time was with 150k miles and my most recent times with a couple extra mods were faster after correcting for altitude. So it's still a tight engine. 
The transmission I can't comment on since I have a T45. I've never felt Ford automatic transmissions were very good, but if taken care of it will certainly last. The problem with a SN-95 is that it is going to take a lot more work and money to just make it even with a S197. You would definately need a converter and gears, and about 120hp just to get low 13s like you want. Sure, it might be reasonable to get a SN95 to the mid-high 13s, but after that it gets really difficult... especially without a power adder. Heck, even looking at the 99-04 cars, how many are NA and run very low 13s-high 12s? VERY FEW and they all lots of engine work.
The transmission I can't comment on since I have a T45. I've never felt Ford automatic transmissions were very good, but if taken care of it will certainly last. The problem with a SN-95 is that it is going to take a lot more work and money to just make it even with a S197. You would definately need a converter and gears, and about 120hp just to get low 13s like you want. Sure, it might be reasonable to get a SN95 to the mid-high 13s, but after that it gets really difficult... especially without a power adder. Heck, even looking at the 99-04 cars, how many are NA and run very low 13s-high 12s? VERY FEW and they all lots of engine work.
