Mercedes put a different water pump pulley and belt on the 3.5L engines to spin them faster. It wasn't to increase cooling, it was because the 3.5L engine had a significantly lower max RPM (4400, I think) and spent most of it's time at 10% lower speeds! I wouldn't mess with that. The stock cooling system should be more than adequate if maintained properly. Install a 603 Turbo radiator if that's larger/different but leave the rest alone.
The head "hot spot" issue is a load of crap, IMO. The original turbo heads were all flawed. MB redesigned them FIVE TIMES (that's six different heads). The later ones have almost no cracking problems. I'd forget trying to pump up a non-turbo 603, and swap in a 603.96x and be done with it. That'll give you 148hp stock, and with the Mosselman intercooler kit, you can bump that to ~175hp.
