Two steps forward ... Hopefully they used the latest version of the engine, but it's hard to say, I imagine it has to be compatible with the PCM and all wiring harnesses, so they would minimize any spec differences between old & new, if such differences exist. Might have gotten the updated valve covers with it, easily checked 
The trans may need a teardown, or the PTU (or RDU) may need to be replaced. Can't get any more definite than that at this point tho, I don't think ...

The trans may need a teardown, or the PTU (or RDU) may need to be replaced. Can't get any more definite than that at this point tho, I don't think ...