Am I in trouble? How bad is this for the engine?

I took out the right exhaust + intake and left intake shims out, went out for a break and came back to rotate the engine for the final valve before realizing the atrocity I had committed. 

I would now have to rotate the engine again without again the shims to put any sort of shims back in!

What's the best move?

Don't panic! All you need to do is re-time the valves, following the instructions in the manual.
Do you know if the timing chain skipped any teeth on the camshaft sprocket?

So I managed to get all the shims back without rotating (maybe a little) the engine, for one of the buckets I had to rotate the cam lobe about 10 degrees counter-clockwise, I hope that didn't mess anything up too bad. I couldn't see and damage on the cam lobes they seemed quite smooth. It looks like no great damage was caused luckily.

As to whether timing chain skipped any teeth? ...Is there any way to know for sure, when I rotated the engine it seemed to go quite smoothly.

And I've never re-timed the valves before is it a difficult process?

No reason cam timing should be off but it just takes a few minutes to check it.

Rotating the engine doesn't change timing. It can scratch up the cam or the bucket.
Cool.
Buddha.

Awesome, thanks for the help everyone. Everything looks fine, gonna put in the new shims and wrap everything up  .

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