I have an 04, had everything that should go wrong with it, go wrong. I agree the silicone boots could be what you are hearing. RiffRaffDiesel was the best price and quality for the boots. A tuner would be a great investment, as long as it has diagnostics. I have the Hyperpac from HyperTech, it improves performance, fuel economy, monitors much more than the gauges and tells you when the dealer is ripping you off. Plan on a front end, turbo, egr cooler, oil cooler, egr valve (at least cleaning it), some injectors, fuel pump blue spring kit & FICM power supply, beside the regular maintenance. Oil changes & fuel filter changes are a must, I use Schaeffer's 700 15W40 and it makes a difference. The engine had no sludge when the egr cooler & oil cooler were replaced at 129K. Good luck.