My question would be where did you get the pump? Genuine OEM Mimaki pump or cheap Chinese made aftermarket one? The cheap aftermarket ones are notorious for not working right. If a pump is not sealing closed properly the head when parked over the capping station can simply wick all the ink out of a cartridge.
I'm assuming this is on an older JV3. This cannot happen (near as easily anyways) on a newer JV33 since the newer machines use a valved ink system and ink cannot flow unless the machine opens the valves behind the cartridge. On a JV3, the ink system is gravity based which is where this is a high possibility of happening.
First of all you need to determine exactly where the ink was coming out. if it simply filled the waste ink tank (and overflowed it) then your problem is either the tubes from the pump to the waste tank, the pump itself (or the tubes that go through the pump), the tubes between the pump and capping tops (quite possible you pulled one off the bottom of the yellow top when installing the pump), or the capping tops. If it leaked our elsewhere then it is simply a matter of finding where the leak is and fixing that.