If you're planning to repaint the MR Y to match the Red version... you're in pretty good shape since the MR Y is somewhat based on the Red version (even though it's painted more like the Gold and has many detail differences). Here are a few thoughts...
Cockpit: The MR cockpit and canopy are built to replicate the Red Y-Wing, including panel lines, plating details and the shape of the front "air scoop" area (all fo which are different on other Y variants). In addition, the panel lines on the canopy are accurate to the Red Y. If you are planning an exact replica of the Red Y - you should note that the real Red filming miniature does not have a cockpit interior (at least not as the model currently exists). I think it will be nearly impossible to remove the interior from the MR Y wing without destroying it. You may have to settle on keeping the interior. The cannons on the Red are a differnt part than the common messerschmidt guns.
Fuselage: As has been said in other threads the details on the MR Y are an amalgamation of various Y versions. Other than individual greebly differences the main thing to do IMHO is replace the R2 unit with the Lancaster part as you already mentioned and the 8-rad neck details need to be reversed. The Red Y has the engine pan part on the port side while all other Y versions have it on the starboard side. I think the MR version has it on the port side, like the Gold Y. I could be wrong about that depending on the final MR design. If you're a real stickler for accuracy the other good news is that the MR Y has a neck length that matches the Red Y. The other Y variants have a neck that is amount 5mm longer than the Red variant.
There are MANY differences in greebly details especially on the sides of the fuselage. For example there is part of an X-Wing R2 strip on the starboard side under the engine pylon (which is great if you have an extra CC X-wing laying around). It appears to have replaced some lost details since it is painted a different color than the main fuselage. As you can see in ref pics this occurs in many other spots as well.
Engines: As you said the starboard engine is very different in terms of details. I wonder how hard it will be to detach the engines from the MR Y, if someone was so inclined?
These are just my thoughts, would love to hear others too.
Dan