In so far as the very narrow sidewall is going to offer less cushion from
the road than a taller sidewall, yes your selection can be affecting your
ride. If I recall correctly, your truck came standard with something like a
32" tire mounted on a 15 or 16 inch rim. That sort of tire would offer you
about 8 inches of sidewall, but you have changed to a rim that gives less
than 6 inches of sidewall. This will give a stiffer ride. You could have
opted for a larger rim AND a smaller ovarall diameter -- say the new tire is
a 31, for example -- this would scrub away another half inch of sidewall,
making the ride that much stiffer.

What sort of tire pressures are you running? I am not completely familiar
with that combination, but my guess is you ought to be running at about 30
to 35 psi.

The Sports Package will also offer a stiffer ride, but you would have
noticed that long before now. I do not know the spring rates, but softer
springs will make the ride more pliant -- albeit, more unstable laterally
(body roll is kept in check to a certain extent by stiffer springs). The
shocks can be changed to a softer shock, and that may help. But softer
shocks will allow the tires to bounce and the body to roll. When you are
driving on the freeway and see a car where the body is moving up and down,
or a tire is bouncing along, this means the shock is worn out and not doing
its job anymore. A softer shock is merely a shock that is between worn out
and the stiff a.s shocks you have.

 You don't mention what size wheels the vehicle originally came with. You
also didn't mention tire size. I will assume you had 15 or 16 inch wheels
stock. The shorter sidewall on the 18" wheels is probably the cause of the
harsh ride. Also check your tire pressure, too much pressure will also cause
a harsh ride. If you have your stock tires and wheels I would put them back
on for a comparisson, if not maybe your brother would let you use his tires
and wheels.

  > SR5 and the suspension on that is better in terms of comfortable.

I'm guessing the truck came stock with 16" wheels and probably P265
load range B tires with a max tire pressure of 35 psi.  The lower
sidewall of the 18" tires is most likely contributing to the harsh
ride.  You didn't mention if this is a 4x4 or not.   At this point the
cheapest solution if you are handy would be to go with a set of shocks
like the Monroe Sensitrak line.  They have a lifetime warranty and
work well on short wheel based vehicles like the 4 runner.  I ran a
set for years on my 90 4 runner after pulling off the Rancho 5000s
that were on it with 31" load range C tires.  The Monroe shocks made
an amazing difference and still worked decent for basic offroading.
The second suggestion would be to go with the stock tire or a
flotation tire like a 31" or 32" but that will require new wheels as
well so the cost becomes a factor.  When running a non standard tire I
always run them at a pressure that allows for maximum tread contact
across the base of the tire when the tire is warm.  This will provide
the best grip for handling and braking, too much pressure will make
the ride stiff and also cause the center of the tire to wear faster
than the outer edges.