The pump gets hot (the Ford manual states that the pump should not be run for more than 2 minutes) - but does it make a noise as if it's working correctly ?

If so, then it's either a sticking relay, dodgy wiring, as raggey says a dodgy pressure switch (that the 5 pin plug fits to), or perhaps it's an issue with the accumulator, the high pressure line, etc, etc.

As standard, the pump takes its feed through a fusible link, not a fuse. If the wiring has been replaced, then potentially the pump is not now fused at all.