[Creeper]

That is one of the weirdest setups I have seen are there any rubber air pipes if so change then to hard pipes. Plastic and rubber flexes and can cause boost leaks or spikes. a more direct air intake to the turbo and from the turbo to the intercooler and from the intercooler to the engine is a good idea. I'm not sure the hard pipes to the intercooler would work well check ebay for a universal kit that you could cut up and rought yourself this will help greatly. Hard pipes can increase hp as they do not flex. If the intercooler will not accept the piping where it is (it looks like it is on top of the motor. Try and relocate it either to the side or the front of the vehicle this will help lower your air temps. For filters I'd suggest a AEM dry flow which has been used in desert or off road racing so no dust or water will get in.