You are nearly there! Theres two valves called by-pass valves that you should see going into the bulkhead of the engine bay, assuming these are blocked, the heater matrix wont get the hot water.
If you do a search you will see these could be the fault and the solution is to remove them in place of straight copper pipes (22mm). However, VW added these valves as a recall as the Mk2's heater matrix's had a tendancy to let go, moreso, burn the passenger's legs by dumping hot coolant on them.
I wouldn't fit the copper pipes, either try a reverse flush to clean them to see if it makes things better or get some new ones.