A few things from my own experience, not an exhaustive list! Look for merc or Indy merc history, check thermostat (should sit at constant 85-90c, often they fail and need replacing - not a big job c £100-£200, but probably the most common fault with c220.
Check for body work rust but should be fine post 2004.
Alloys may well need refurbish and might be peeling / bubbling. If they have been refurbished check how well and whether they were painted or powder coated, if painted be aware that they will detiorrate again of surly quickly.
Check automatic sensor on passenger seat is not faulty (by leaving seat empty and ensuring seatbelt warning light goes out ) this sensor is designed to deactivate airbag if child seat is in place but sensor goes faulty and needs expensive replacement £400 or can be bypassed with a resistor on eBay.
Check stable engine idol at stationery, if it's uneven this can be (a) mass airflow sensor (b) build up of diesel residue through injectors - this should be fine at 50k.
Overall 2005/06 cars are good and not many issues.
Nice choice the CLK and the 220cdi is a little crude but a workhorse engine car should easily do another 100k without too many issues- good luck