I have a 2" lift and 31x10.5 A/T's on mine. You can tell it's lifted and I have plenty of clearance off-road, but there doesn't seem to be much fender clearance from afar. Here's a couple pictures of my YJ from slightly different angles for you to compare to what you're looking for.
If you look closely you can see where my tires have rubbed my fender flares a little when I've been off-roading (they're deformed in places.) You might want to consider TJ flares or wider aftermarket flares if you go with a 2" lift or stay with the 1" lift you've got. Still, I get no tires rubbing on metal even when I'm at high flex. My YJ doesn't flex as good as some but it's not bad either.
Also, keep in mind, if you're running the 4-banger/5-spd and you go to 31's on stock gears, you'll top out at about 70mph in 5th gear on a good, flat highway. And that's a conservative estimate, many people say 65mph. With the mods in my sig I can get her up to about 75mph in 5th with a tail wind on flat road, ~70mph otherwise. On a slight incline I have to shift down to 4th to maintain 65mph. On steep inclines I've had to go as low as 3rd gear to maintain speed (~50mph.) Just something to consider.
