Just work on the basis of the information recorded in the "Vehicle Details" section of the registration document, and the information required in the "Changes to Current Vehicle" section..
You need to tell the DVLA if anything pertinent has changed (or if you have made such radical changes to the chassis that an IVA is required, but that's a different issue entirely). There is no entry for turbo or N/A and there is no entry for manual or auto, so just tell them about the engine number change and let them decide whether they need to check the engine's provenance, but be prepared to show that you acquired it legitimately.