Ok, follow up and a couple of additional thoughts on the water pump job. I finally got all the parts middle of last week and starting Saturday morning I got back after it. Generally speaking the re-assembly is a lot easier that the dis-assembly. Things are cleaner and you basically know where everything goes, etc.
I had one major close call installing the water pump as I was going to reuse the bolts and when installing everything to 89 in-lbs I had one bolt that was taking more turns to tighten and as it was snugging I heard a small pop. I was using a 1/4" drive torque wrench and fortunately I was going slow. While I thought I had potentially broken the bolt, I was able to back out the bolt with my fingers and luckily though the body of the bolt had broken the thread was still continuous and I got the whole bolt back out. Examining the bolt I found it was significantly elongated in the threads around the break and I just didn't check it close enough before re-using it. I removed the other 6 bolts I already had in and found two others with some thread elongation but nothing like the first one that snapped.
The elongation on the bolt that snapped was about 2mm and the others were about 1mm. With the pitch of the bolt I can't see you getting this much elongation at 89 in-lbs + 45 deg. I'm 99% sure I didn't rotate multiple bolts 1-2 extra turns at full torque (which is that the elongation looked like) so I'm assuming it came that way. But I ended up pitching all the WP bolts an getting new ones from Ford on Saturday morning. Maybe this is a no brainer for everyone else, but I'd definitely recommend going with new bolts for the WP based on what I saw.
After burning an hour with the extra WP work and the run to Ford, I got back at it and the timing kit went on smoothly. I had to fiddle the cams a few degrees with a wrench to get the phasers back on but it was pretty straight forward. Thanks to the notes in the other thread and the piece of paper that came in the timing kit I knew about the need to release the secondary tensioners by pressing them down. I ended up replacing the phaser bolts, secondary chains, secondary tensioners, main chain, guides, and crankshaft timing sprocket. The Cloyes kit came with a main tensioner, but it just seemed very cheaply made. The one I got had a rough casting and the shaft had a little play so I ended up cleaning, inspecting and reusing the original main tensioner as it seemed to be in good condition with good spring force.
Putting the front cover on was easier than I thought it would be after taking 3-4 practice runs. I left the AC line connected but pulled back and zip tied, I stood on a cooler to have really good top down visibility and after a few tries I could guide the engine cover into position without rubbing the gasket side on anything. I did two things which made it easier from my viewpoint. The first was I used some PVC pipe to make a good handle on the cover using two of the engine mount studs. This gave me a good solid handhold for moving and tilting the cover while using my other hand for finicky parts of the move. The second thing I'd say is that while you could do this without the guide pins, I realized quickly that trying to line up the crank and the rest of the cover correctly was not easy. I fabricated two wooden dowels sticking out about 3" to use as guide pins and it made the whole job much easier.
With the guide pins, you lower the cover down keeping plenty of clearance and once its down to the right height, you tilt the cover forward at the top to engage the guide pins. Once the pins are in the holes, the whole cover slides forward easily and the two pins keep it aligned pretty much perfectly. While I wouldn't necessarily order the $50 alignment pins listed in the repair procedure, I second the recommendation made by someone else to get two new bolts and cut the heads off a pair of old ones to use as guide pins. The dry run after putting the pins in was so much easier than the 2-3 before the pins.
After getting the cover on, I did the race to install all the bolts. I had my bolt board ready with all the bolts cleaned and in their slots. My wife helped me out by handing me the bolts in order and marking the ones I had torqued so other than a bunch of up and down it went pretty smooth. From there it I went ahead and installed the belt tensioner since it was easy to get too at that point and then went to the engine mount and valve covers. Everything went smoothly until I accidentally pinched the alternator main lead under the edge of the LH valve cover. I had left the negative battery lead accidentally connected after unlocking the doors and as I tightened the cover down I got a bunch of sparking and hot wire smell. I yanked the neg terminal and that stopped it, but it was late on Saturday and it wasn't immediately obvious what it was so I called it quits for the night.
Sunday morning had me checking things with good light and I quickly figured our the alternator wire was pinched. It had gotten pulled into the valve cover as I moved the wiring harness around putting the cover on. The retaining pin on the harness that runs up the left side of the cover had caught on the alternator wire and I didn't notice when tightening it down as the pinch was directly under the harness. With better light I ran my fingers around the cover and could immediately tell the alternator wire didn't have any play. Removing the cover exposed the pinched insulation. I repaired it with some self fusing tape and some plastic spiral wire loom for a little extra protection. Testing after that seems to indicate no electronic or electrical issues, so I think I lucked out.
After that it was all down hill. Reinstalled the LH valve cover, inlet manifold, and the rest of the parts. Double checked the oil pan was fully drained, swapped the filter and filled the engine with clean oil, filled the coolant and reinstalled the fuel pump fuse. After a few cranks it fired right up and I went through the coolant bleeding procedure. The first few times I ran it I got a little worried as I had a fair amount of smoke coming up from the engine bay, but after a little inspection is was just a little bit of oil from the rear cover which had dripped on the exhaust manifold. The smoke cleared up after a few 2-3 minute runs while bleeding the coolant.
After that I took a short test drive around the block then checked all the fluids and found no issues. So then I took a 15 minute drive with about 8-10 minutes on the freeway at 65. Stopped and check everything again with no problem and headed home where I took another look and didn't see any drips and the fluids looked good. So a this point I think I'm good and saved several thousand doing the work at the end of the day.