Auto is nice offroad, but the 1st is higher than the
Man Trans, and the 3rd is lower than 5th on a Man
Trans.
Man Trans has 5.12:1 Diff Gears, Auto has 4.62:1
so use the Man Trans Axles/diffs in the Auto and
it will help for bigger tires
As far as Bad Noise

I'd have to hear it, a rattling
noise to me, I'd say that if I were describing a loose
heat sheild on the exhaust, a knock when the cylinder
is firing is a bad thing, unless it's piston slap, then it's
just a normal worn engine sound.
How many miles, would help to determin the problem too.
Wild