These are the steps that need to be taken next:
1. "Intialize the limit". After doing this step, go into service mode and do a test print. Ignore the test print results, but instead check the cap to head alignment. Do this so you can see where the machine parks the head through the normal operation. If the alignment is off, note which way and how much. To adjust this, move the print carriage out of the way and do steps 7-10 in the "Initialize the limit" document. Run the "Intialize the limit", restart in service mode , do a test print and observe the cap/head alignment. Once the alignment is perfect, do the cap height adjustment.
2. Do a power clean, observing the clear line coming from the M/Y cap, watching for ink coming through that line. If you are still not getting ink through that line, disconnect it at the Y fitting, put a syringe on the line and pull gently. If you are pulling air or ink with air bubbles, then I suggest you replace the cap with an Roland OEM cap. Using aftermarket caps are like rolling the dice, with a good chance of getting a poorly manufactured one.
Please post the results and I will advise the next step.