In Print Studio Pro, did you make sure that "No Color Correction" was turned on? If not, that could be an important cause of problems. Have a look at my Canon Pro-2000 review (much of which should apply to the Pro-4000 as well). PSP should work well according to that research. ACPU may not be all that useful, but no harm trying it. Can you print targets from i1Studio? If so, may be worth trying that.
Anyhow, you are right to start the troubleshooting at the level of printing the targets, so will be interesting to see what you come up with.