Aligning Timing camshaft sprockets on Mitsubishi 3.0 engine.

I sent both of heads to be checked for cracks and cleaned. The removal process for the 3.0 engine doesn't call for the disassemble of the rocket arm and shaft assemblies. It states that they must be inspected and if damage or wear is evident, replace as a single assembly. So, when I took it to the machine shop they completely disassembled it in order to test and clean it. After testing they found that both heads were warped slightly, but repairable. They also had to replace all 24 of the lifters due to them falling apart. They informed me that the camshaft sprocket were placed back in position with the timing marks lined up. Note. They didn't have the valve head covers to do this with. After bringing the heads home I placed them on the work bench side by side with the valve covers on to determine if the timing marks line up. The timing marks on the camshaft sprocket for the back head is not lined up with the timing marks on the head cover where it should be. The number one cylinder is TDC and the camshaft mark is dead on. The front head camshaft sprocket is lined up perfectly as it was when I took it off. I placed a ratchet and socket on the back head that wasn't lining up and turned it clockwise. It will not line up with the valve cover marks. I returned it back to its original position and turned the head on its side to see if all the exhaust ports were closed in what I'm calling a misaligned position and they were. I'm not sure what to do.

My question is. Was the head assemble put back together wrong and how do I get it aligned correctly?