Intercooler is the easiest part of the coolers to clean. To clean both the air sided and water side you need to remove it from the engine. Once off the engine. you will likely find a build up of dirty engine oil in the bottom of the cooler. There is a drain screw to drain that while its still attached to the engine but since I have it off I can poor the oil out the intake ports. The dirty engine oil comes from the crankcase ventilation system that is drawn from through the turbo and back to the combustion chamber through the aircooler. Below you can see the dirty engine oil in the manifold the feed the air to the intercooler.
The fins on the watertubes will become coated with this residue over time and should be cleaned off. The picture below shows the dirty fins on the inlet side of the intercooler. I use mineral spirits in my shop solvent tank to soak and rinse off the oily tubes after I pull the core out.
Pulling the end caps off the intercooler will allow cleaning of the water side, tubes and end caps. Residue from the zinc anodes and some marine growth will collect in here. The corrosion and marine growth buildup under the "O"ring seals cause seepage of seawater to generate copper carbonate and corrosion at the aluminum housing. Another reason to pull the units apart rather than just flushing the engine with Barnacle Buster.
After pulling the end caps, stand the unit on end with the end that has a bronze flange facing up. A couple of taps on the top of the aluminum housing with a wood block will break things free. The the core can be carefully pulled out for cleaning. The corrosion if any on the aluminum parts only seal air so it isn't a huge deal if it doesn't clean up real well. The bronze surfaces on the core and endcaps must be perfectly clean and no scratches across the sealing surfaces.
Rinse the air side of both the housing and core with solvent to remove the oil. I reassembled the core and housing with the end cap on the flanged end and then filled the water side with vinager to disolve the marine growth in the core. Disassemble again to thoroughly rinse and dry everything. Polish the sealing surfaces if necessary and reassemble with new seals.