I've been running 35's on my 2000 TJ for 4 years now, and it has an automatic tranny and I haven't had anything done to the gears...? How come I haven't run into any issues...? I run 90% on road and 5% off road...  

i would change gears to get better gas mileage also if you havent bought a new spedo gear to correct the difference in tire size id buy one of them too.  

the only issues there are is the massive loss of power and economy, the tall gears will acually help keep it from snaping axle shafts due to the lack of power to the ground.....

also you have a three speed tranny...which means a 1-1 tranny ratio... and may have 3.73 gears, which are nearly suficient to run the 35's (about 2350rpm @65), however still lacking on the take off. 4.10 gears would be much better for a daily driver that doesn't see prolonged high speed driving.