The p0300 is a random misfire code and the two other are transmission codes. I would start with a crank case relearn and once it is running if you still have the issue see if the exhaust smells like eggs. The dealer should have checked the EGR and O2 values to see if they are not responding like they should.
How did they determine it was the valves did they do a compression test?
What did you keep from the original engine?
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