I would give the motor an acid flush with muratic acid. You can take off the side plate or flush it through the thermostat housing. If your engine has been raw water cooled for a number ofr years there is a good chance that there is some scale inside. You would definitely want to try to remove that before enclosing the system, although it would work either way of course. I would also change the water/cooling fluid after the first couple of times you use the engine once the FWC system is installed.