Manifold water jacket locations

I have a 2004 chevy imapala 3.8, took the upper and lower manifolds off and there are 4 coolant holes around the 6 cylinders, 2 on each side the one on passenger side in the rear was plugged with what reminded me of particle board, I removed it easily, now on the manifold there is just 2 holes both on drivers side one in front and one in back, on the passenger side front there is no hole at all it looks to be aluminum. On the passenger side rear of the manifold, looks like a hole should be there but is filled with very hard junk like I dug out of the engine but it is not coming out so easily and it doesn't look like there is a water channel there anyway. Are all these holes suppose to be open or is this junk suppose to be in there clogging holes? And how many open holes are in the manifold?