I did the same thing on my rebuild.
I read that the bolts are all re-useable.
The only thing I did replace was the cylinder head bolts.
I'm a little over 3500 miles on my rebuild, and it's still going strong.

I was told my jeep with the stock 31in tires, and 4.10 gears had more pep than a JK with about 100k miles, 5.13 gears, and 35in tires.
I'm sure it's the tire weight, but it makes me feel like I accomplished something.