Changing the gear ratio means pulling both differentials apart and replacing the physical gears in them. If you've gone to larger tires, you probably should do this.
Modifying the computer is done to correct the speedometer and such for the new gears and wheel size. You should do this if you've...
If your needs include other brands, I recommend the BlueDriver. I leave a JScan dongle in each Jeep and a BlueDriver in the Vette at all times. I keep one of each in the garage for working on other peoples junk.
You just download JScan, and purchase however many VIN licenses you want. They're cheap. There's a list of recommended OBDII dongles on the JScan site. Buy one. All told, JScan and the dongle are well under $100.
Step 1: lose the steering dampers. All they do is mask problems. Then start checking to see what is worn or loose. How much play is there in the steering wheel? Now check that for everything else in the steering and suspension, not just the wheels.
Get off the fence and onto the 4.56 gears. 4.10 is less than ideal for the highway. You don't have enough power and your mileage and performance will be less than they would be with the 4.56.
This. ANYTHING can be fixed, if you're determined enough and willing to spend the money. But it might be cheaper to replace. Check prices for used tops in your area, then drop by repair shops for estimates. Then check with your insurance.
If you look in the How-To section of the forum, I did a fairly extensive write-up on the first install I did. It's pretty straight forward and there are no special skills or tools required.
[Addendum]Here's a link to the How-To article...