No, dude, it's not screwed up! It's all good!And everybody that followed your how-to is all good too. I wasn't saying it would cause a misfire I was saying if there's a misfire it would be attributed to the wrong cylinder which might cause some confusion when it came time to diagnose the problem. But in no way was I saying installing the timing belt according to your instructions will cause misfire or poor running.
Background info: These engines are even fire V6s so there's a power stroke every 120 degrees. Firing order is 123456 with 1 & 4 paired, 2 & 5 paired and 3 & 6 paired and by that I mean rising and falling together so that while one is at TDC at end of compression stroke, its mate is at TDC at end of exhaust stroke. The ignition system is set up so that the pairs share spark. The one that's on the compression stroke goes bang when it gets spark. (and a few degrees later will be into the power stroke) Since the other one is on exhaust stroke the spark does nothing - it's wasted.
The PCM uses two sensors to determine which cylinder is firing - one to determine crank position (that narrows it down to two) and one to determine camshaft position (that tells it which one of the two is on power stroke and which one is on intake). When the PCM senses sudden drop in crank speed (i.e., a misfire) it assigns it to a particular cylinder, keeps a count of the misfires and if there are too many, throws a DTC implicating the bad cylinder.
The belt change TSB has you align the valves and crank for #2 at TDC on compression stroke which means it's mate # 5's valves are positioned for end of exhaust stroke.
Here's why I said the PCM could get the cylinders confused: I know from working on bikes with wasted spark ignitions that as long as you've got the crank right, you can set the valves up 180 degrees off and since there's a spark every time the piston is near TDC, the bike will fire and run perfectly because the with the next turn everything will line up properly for compression stroke. If the VX runs with crank 180 degrees off like in your pictures then the PCM would be sensing that #2 is firing when in reality #5 is firing and thus if there were misfire it would assign the "blame" to the wrong cylinder. I was thinking it actually would run like that because when you set up the valves like the TSB says with #2 at TDC on the compression stroke then #5 is at TDC on exhaust so the exhaust valve is open and intake is closed. Then if the crank is positioned as per your pics, with the next turn I think both valves would be closed in #5 and what used to be a wasted spark during the exhaust stroke is now happening in the compression stroke - so it fires up and runs fine - but the sensors are telling the PCM that #2 is firing when #5 is firing and vice versa.
I'm thinking more clearly now than at 2AM last night though and am now doubting it will run with the crank 180 degrees off. The problem is I mostly work on singles and when you throw in multiple cylinders and DOHC it warps my mind! Or what little is left of it. I totally suck at visualization in 3D. I'm gonna have to draw some pictures I guess!
To be continued...