Adding a high flow air cleaner and a tuner will have a huge impact on performance for you. The tuner is the only way your going to be able to be able to make adjustments and get rid of the popping. Being that your 05 is an open loop system your best bet on a tuner would be a Power Commander. It is also easiest to find a professional tuner to put it on a dyno and build you a custom MAP. DynoJet will also send you a MAP that is usually at least 95% right without the expense of putting it on a dyno.
The popping is normal and even happens with stock pipes, they just muffle it so you don't notice it.
As the others said, look it over and make sure you don't have an exhust leak as that will cause popping also.