A bent valve would not throw off timing, but off timing could bend a valve. What I find odd is that you have no compression in only that one cylinder. You are allowed to be off a tooth before you bend a valve. Car just would not run as good as it would with correct timing.
Do you still count 16 links on your timing chain, between the 2 cam cap marks?
And the marks you made before won't line up simply because they won't after rotation. Forget exact thing that makes this happen.
Also, did you not notice the misfires with one missing cylinder? Easy way to test to see if that cylinder is indeed dead, disconnect ignition coil #3 when car is running (if you even want to attempt this). If the car cuts off, then you have an issue with cylinder 2. If it stays running, then you did the test incorrect for that cylinder. DO AT YOUR OWN RISK!!!
When you bend a valve due to timing being off, it would usually bend the same valve in every last cylinder head the same. Usually it is the middle intake valve. Before doing anything, confirm timing with everything and post up your results (damper with TB cover, exhaust cam gear mark with VC, both line up with cylinder 1+4 TDC, and cam notches line up with the cam cap arrow). Unless the tensioner is fully tensioned in the up position, the marks will be slightly off (what I'm thinking happened with you). As long as you have the 16 links and they both look damn near close, you most likely have it correct.
Pics always help.
*I find it really odd you lost compression in only one cylinder from timing being off.
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