I might have tried aligning the cams by rotating the crankshaft as described in the manual the first time I tried it but I really don't remember. Usually, as I mentioned twice already
: I just align the camshafts to the required positions as shown in the manual and go from there. The nice thing about doing it this way is that you don't need to look at the T mark at all, and you know that you will be on the compression stroke simply because I assume that the cam sprockets are correctly positioned on the cams.
I was going to put this off until next spring but since it has been over 20K miles since I did the last check I thought I'd dive in to see how mine worked...
I can confirm that I was able to follow the procedure as outlined in the manual to rotate the crankshaft CCW as needed to get all four of the cam positions to line up as shown. I took a series of pictures showing the position of the cams for both the right and left sides of the engine for each cylinder tested:
No. 1 TDC: Right Bank No.1 TDC: Left Bank
No. 4 TDC: Right Bank No.4 TDC: Left Bank
No. 3 TDC: Right Bank No.3 TDC: Left Bank
No. 2 TDC: Right Bank No.2 TDC: Left Bank
So after looking at my valves I can say that one pair of your valves is rotated 180 degrees out of phase as has already been mentioned. In your case, you suspect the left side because that side was worked on back in 2009. Theoretically, due to the symmetry of this engine design, you could have the same mixup done on the right hand bank and you would observe the exact same symptoms that you currently see. The true timing generation is performed by the cam position sensor which is located on the right intake cam IIRC.
After looking in the manual I saw that the pulse generator ring is keyed so that item cannot be mistimed. The other interesting thing I noted was that positions of the cam sprockets on the bank opposite the cylinder being tested, were not as shown in the diagram in this
post, i.e. testing No.1 cylinder by aligning the left bank cams but looking to see what position the cams on the right bank look like. The diagram shows positions for both cylinder No1 and No2 TDC. You will note that in both cases, the cams on the opposite bank are 180 degrees out of phase with that shown...
(certainly seems like a documentation error to me)
.
I guess I'm still at somewhat of a loss as to how your bike has performed since you had the shims replaced in 2009. Having the cams off by 180 degrees obviously doesn't damage them physically when the engine rotates but the problem I see you having is that the engine is going to be injecting fuel into two of your four cylinders right when the exhaust valve is opening. It is possible that part of the air/fuel mixture might remain in the cylinder after that and since your going to get spark on both cylinders, you might get some power out of that bad side.
Is the exhaust (catalytic converter) pipe discolored on one side? I would think that you are dumping a lot of unburned fuel into that exhaust on the bad side. Do you have any popping sound coming from the exhaust?
It would be interesting to hear how your engine runs in person. Keep us posted on your progress...