Notnilc20,
Looks like you're going straight into it - good for you. I've had parts taking up 4 shelves on a rack so i totally can relate to the dizzying sense of it all. Stay organized, tag everything, take pictures, and take notes on a notepad. I had to do all that just to stay sane! 
As far as the egr goes - best to remove it completely since its already crimped off. I purchased the following block off kit from ksd but as others mentioned above you can make your own: 
http://www.ksdengineering.com/KSDEngineering-EGR-Blockoff-Plate-w-Gasket-_p_59.htmlMore importantly however, the thing that really concerns me is 2 fold: 1) You said the crank was really hard to turn (which should not be the case. If anything, if you have a 1/2 inch ratchet you should be able to turn using 1 hand and it should be smooth in between stroke. 2) If you said water came out with oil then that def points to a blown head gasket. Thus allowing the water and oil to mix, which also prolly means water got into areas of the block it obviously shouldn't have. I'm interested to see what the cylinders and pistons look like once you remove the head. 
Instead of spending more monies as someone rightfully noted above, I think it would be best to ditch it and grab a 20v or another 16v that you know is properly working. I'm all for keeping the 16v even with limited power but the 2 things you described above leads me to believe that there's more internal issues not worth trying to resolve. I wouldn't want for you to waste all this money when you can simply pick up a functioning engine for same price.