OK so if you have a new head, and it is printing ok for part of the job then you can rule that out. There isn't anything after the ink or head to go wrong. If the head is getting the correct supply of ink, then it should be printing ok.
Are the test prints on the new head ok, and did you also change the damper when you changed the head? The seal to the damper can sometimes leak air which will starve the head of ink. It could even be a bad ink cartridge that isn't making a good seal.
What I would do next is swap the yellow and magenta dampers over onto the head, so magenta ink is going to the yellow head, and yellow ink to the magenta.
Run a job printing large squares of just magenta and yellow ( it will take a bit of printing to clear the old ink out of the dampers and ink head ). When the yellow head is putting out magenta ink, print out large blocks of yellow artwork and see if it prints properly with no ink running out, then do the same with large blocks of magenta artwork and see how that works.
If the magenta prints fine then you know the yellow head and all the signals getting to it are fine as the printer thinks it is printing in yellow.
If the yellow prints fine you know the ink supply to the head is ok, and the problem is elsewhere