Your biggest problem is the fact that it uses a speed density computer which will not make any adjustments for increased airflow thru the motor from ported heads,bigger cam or other mods. To make more power you need to get more air & fuel into the motor....getting the air in&out is the easy part but adding the required fuel is the tricky part. Yeah you can add headers,exhaust,free flowing intake stuff the help it breath easier but the power gain will be very small and most likely only from making the engine run leaner.
The 2.9 is OK motor but tryin to get serious power out of it is pointless. I think the best and easiest option is to re-gear the truck and multiply the little power it already makes.
2nd best option is a motor swap. A 4.0 is a major upgrade over the 2.9 but your still stuck with a garbage trans. Swapping is a 5.0 is alot more work but it opens up your options for a much stronger drivetrain like c4's,c6's or even AOD's.