Here is what I know about Charge Air Coolers (CAC).
1. they are fragile compared with radiators
2. they need to be cleaned with "gentle" water pressure, not pressure washers
3. they can develop cracks due to overtightening of those special clamps (which are designed to NOT overtighten but you know...)
4. if one cracks, it must be repaired or replaced as you will lose a significant amount of power and possibly damage the turbo.
5. the CAC is designed to cool and thus aid in the compression (further) and efficiency of the incoming air charge prior to fuel atomization and then combustion. CAC equipped turbo-diesels have more power than non-CAC equipped ones.
Mine doesn't have any cracks (that I know of) but I am still trying to remove all of the slobber tube grease (before I lengthened the short factory tube). My next step would be total removal and if it comes to that, I will get it boiled out and checked for leaks as well as the radiator.
FWIW, I would have your radiator rodded and boiled out while you have this stuff apart and possibly have the new CAC boiled out as well just in case there is some manufacturing junk left in there.
Re: the exhaust manifold, I have heard of some people having these issues and it is not uncommon considering the heat in the engine bay. Unless there was a mfr. defect, the manifold may have cracked due to overtightening or overheating. In both cases, the mating surface of the head should be checked for a smooth, square surface prior to the manifold being installed (and ditto for the manifold mating surface) plus ALL of the exhaust studs/bolts must be replaced with NEW due to heat temper and stretch issues.
There. You just got a lot of my experience for only $.02. Not a bad deal IMHO.