Absolutely, positively no K&N filtration systems of any kind on your engine.
They simply don't filter enough particulate matter.  AFE's PG7 filters have
been shown (through oil analysis) to work well, as well as the UNI
dual-stage foam filters being used in the Scotty Air Systems intakes.

What's your purpose for looking to upgrade?  More top-end power?  Better
fuel economy?  Quicker acceleration?

There are several different fueling boxes, as well as tuners, available that
work well.  (Fueling boxes are add-on modules that trick the ECM into
delivering more fuel, or delivering fuel sooner - tuners re-program the ECM
directly to alter the fuel and timing curves).  On the low-end (40-70HP),
boxes like the Edge EZ and the Quadzilla XZT are popular add-ons.  In the
mid-range (80-120HP), you have the Edge Juice, the Quadzilla Xzillaraider,
and the Bullydog Powerpup (this is a tuner).  On the high-end (140-200HP),
there's the Edge Hot Juice (just a software upgrade to the Juice), the
Xzillaraider race version, the Bullydog Powerpup w/ their "Crazy Larry"
program, or the TST PowermaxCR (with either the standard program, or the
twin-turbo program).  With all but the low-end here, you don't just slap
these things on and go...  you need to address other areas, such as the
intake (get more air, at less restriction, into the turbo to help lower
EGT's), the exhaust (gotta get all that air and burned fuel out - less
restriction is better here as well), the turbo (stock turbos will run out of
their efficiency range, and/or choke off the exhaust stream, making for high
EGTs), the fuel supply (a higher capacity pump is needed to keep the fuel
pressure to the injection pump in the positive region when adding more
fuel), and the drivetrain (clutch/transmission upgrades are necessary to
cope with the added power).

Entire books can be written on this subject, as needs and goals vary widely
from person to person.  What exactly are you looking to get out of your
truck?