Are you sure you got the timing spot on. As far as the chain jumping a tooth or two you would normally hear it slip when loosening them off. Did it feel smooth when loosening them with no clicky sounds or anything. I would double check you got the timing spot on with the front cylinder. You may have it 180 degrees out. The flywheel has to be turned 1 1/4 turns anti clockwise, so you will see the FT mark once and then when it comes around again it will be 1 1/4 turns.
Stacks being on the wrong way around wont make that drastic a change, but long one goes on the rear and short on the front. You could check your vacuum hose is back in the right place on the tank as it's a simple check, BTBH I don't think this would cause this either, but it's worth checking.
I would check your timing. But the only way to do this is to remove the cam sprockets. You can verify whether anything has jumped teeth by the position of the cam and cam sprockets. You will see an FI for front inlet which should be horizontal to the top of the engine casing.
Her is a pic of the rear cylinder.
The rear sprocket will be the opposite except it will have FE for front exhaust The rear cylinder will have RI and RE.
It's a little harder to see the RE as the frame gets in the way.
So front cylinder will be FI and FE and the rear cylinder will be RI and RE.
If you need to remove the front cam cover it will take you an extra 20mins as you need to remove the fairing, carbs and the plastic cowl below it. Loosen the bolt on the oil cooler and pull it forward out the way, and I think I may have needed to loosen the rads and pull them out the way as well. No need to undo any hoses on these. You can then gain access to the bolts on the front cam cover.
If you don't want to remove the front cam cover then set the rear timing to TDC ie flywheel on RT, then set the front to FT making sure it 1 1/4 turns so so the second time where you see the FT in the little window.
(:-})
). I don't expect to need to adjust them until they have covered about 20,000 - 30,000 which IIRC is the service interval for auto's.
well technically it's in between the two at TDC. 
