Did you ever find out if your last engine was sludged?
It would have made it a free replacment.
Also a person can find it much easier to acess the rear bank of plugs by removing the manifold , i personally have enough tools that i have not done it that way.
I have to agree the computer sounds a bit funny as well.
A misfire is possible as the front plugs have individual coils on top of each [plug. The rear bank has wires going to them from the side an 1 main coil for them ,so there may be a problem with the coil on this new engine.