I put in another few hours today. So far about 4 hours of actual work and I'm just now putting stuff back together. But I am going slow and taking a lot of breaks. I have the whole weekend to finish so not in a rush.
After I pulled the motor mount piece with the bushing (part on the car) I noticed one of the bolt threads were really chewed with threads missing. I went to five places and no one had the bolts. I finally just cleaned the bolts and threads out as best I could with at tap and die set.
I got the new water pump on today and will be putting everything else back together tomorrow. The top bolt on the WP goes into an oil passage. All three bolts had blue thread locker on them so I put more back on using waterpump safe blue from Permatex.
Having the cam/crank lock kit makes me feel a lot better. So far everything is lining up nicely except the crank had to be rotated backwards about a 1/8" to get aligned. My belt tensioner was way out, so the belt was stretched pretty bad at 123,000 miles.
Here's a picture of the bottom cover and the five sizes, yes FIVE different bolt sizes. I hope this helps the guy that pulls them out without paying attention where they went.