I love a story with a happy ending and this one will not disappoint.
I searched high and wide for a leakdown tester, but could not find one in town to ether, buy, beg, borrow, or steal. So we put that issue aside and checked in on this thread. Happy to hear from Ionbeam, Fred, and others, we decided to squirt about 10ml of oil into the #4 hole. I rotated the crank by hand about 5 revolutions to try and circulate the oil. Compression test on this hole bumped up to just under 150 psi. Very encouraged, we decided to press on.
We buttoned up the motor, double (TRIPLE) checked everything, and .....
Once the engine was up to full running temperature, the large hose behind the coolant pipe was seeping a little, so we broke for lunch.
In the afternoon, we were able to sync the Throttle bodies (Cylinder 2, 3, and 4 were all off from #1) and seal everything up. We adjusted the throttle cables and even re-torqued the engine mounting bolts (both bolts for the frame sliders were not tight enough).
We did not perform another compression test to see if things are more normal after the motor is up to operating temp.
I followed Mike on a 40 mile test ride and everything is good to go.
Few things learned to wrap this up:
1. We used liquid paper to highlight the timing marks on the outside of the cam gears. That helped a ton and with a more directed light beam, we were able to use line of sight down the top plane of the cylinder head to confirm good timing.
2. We did transfer some penciled marks onto the inside of the cam gears and that helped to get us on the right tooth.
3. Intech's "leading a tooth" method was the shit and was very helpful in setting the cams on the right tooth.
4. If I was just checking valves or changing the CCT, I would not remove the timing rotor cover. However and otherwise, I absolutely would. There is a plug you can remove to simply turn the crank (you can also spin the wheel with the bike in gear), and there is an inspection bolt that you can remove and look at a mark that is supposed to show you #1 TDC. But for my money, I'll spend the $7 on a cover gskt and see the proper timing mark on the crank gear with my own eyes.
5. A small squirt of silicon spray on the cooling pipe barbs was very helpful in installing the pipe (especially on the big hose).
6. I think this has been mentioned elsewhere, but rotating that hose clamp for the big hose about 45 degrees clockwise makes it much easier to install and tighten.
7. I need to stop over thinking the valve lash. I have some "go or no go" feeler gages. Earlier this week, I called Friendly Yamaha to discuss the situation and see if they would be willing to put it back together if it came to that. This guy told me that DIY mechanics over think valve clearances way too much. The spec given from Yamaha is a go or no go spec. He said that if at 26,000 miles (for example), you check the exhaust and a 0.007" feeler gage can fit in (tight or otherwise), then it is in spec and you can leave it alone. Yamaha offers this spec such that even if the lash is at the tightest point of the interval, then it won't tighten enough over the next 26,000 miles to cause engine damage. At the next check, it will need a different shim. But at this check, it's a "go" and you can leave it alone. Forget about this "loose 7" or "tight 6" crap. It's either a go or a no go, plain and simple.
Finally, and MOST importantly, we couldn't have finished without you guys. Admittedly, we probably wouldn't have started in the first place without you guys anyway. But I'm humbled by your willingness to help. I hope to return the favor in my own way some day. I sincerely appreciate your advice, one and all.
Tomorrow, I think I will go for a ride....
