Fear not. Larger tires will not mess with your gearing.
It certainly changes your effective final drive ratio, and I'm sure it made the truck a dog compared to before. I would highly recommend that you replace with 4.56 or 4.88 gears to get that 'pep' back in the truck.
I had 4.56 gears with my 34" tires, and I wish I had gone with 4.88 gears.
I think it does mess with your gearing if it ruins your final drive ratio...?
The issue with larger tires is unsprung weight... simply stated , it takes more torque to turn those heavy meats and short of supercharging or other extreme engine mods, gearing is the other viable solution.
Gears are torque multipliers but horsepower drainers...that's why your top end speed goes down without boosting horsepower and rpm in the engine.
2 inch lift for 35's? Wow I remember when it took 5 inches to achieve proper clearance...Has something on these trucks changed with age, or are tires getting smaller?