What is the giant (28mm) bolt above and to the left of the Oil Filter?

Engine block drain plug (coolant). There's one on the front of the engine block, also.

I can't find a spot for one on the front of the engine. By front, you mean toward the radiator, right? I didn't notice the plug/bolt when I was stripping the old block so I had to order one. That brings up another question. I was trying to determine if I gooned anything else by looking at the exploded diagrams on thehondapartsstore. They list something called the CVR. Breathing port. I can't tell from the diagram what it is and where it goes.

As you face the engine, it's on the left side of the block (close to the O2 sensor). You may want to remove the heat shield.

You have been very helpful and I appreciate it. I was looking at your PCM test and it mentions checking voltage to the MAP sensor. Which one is the MAP? I'm starting to think I might have a bad computer. I was deployed to Iraq and my son drove the car through some pretty deep water. He hydro-locked one of the pistons. I've since swapped in a new engine, but I'm having some other problems. The engine starts and runs fine at idle. The transmission works well in reverse but in D4 it seems to be in high gear. If I manually shift down it will go in 1rst and 2nd. Additionally, headlights don't work (bulb and fuse check good), A/C; blower and defrost controls don't work, engine doesn't seem to be conpensating for different engine speeds as evidenced by a knock in certain places in the power band (timing is set). CEL and SRS lights are on but I don't have a code reader to investigate further.