After of numerous days spent to find the misfire I decided to open the heads and find out if the problem is coming from inside.
I took the heads to the machine shop, they are going to clean them up and check the compression. The heads overall don't look bad, valves are not bent. The head gasket on the left head was replaced, but the head looked old; the head gasket on the right was bad, but the head looked like new. Weird :/
The bad thing is that the heads were easy to take off, we are thinking they were not on the proper torque.
Question is, what if they tried to mess with the valves and did not do a proper job with it, how can I adjust the valves myself? Any special tools needed?