First of all my respects for this outstanding review, this has got to be one of the most elaborate and well written reviews I've read so far. I enjoyed it thoroughly and hope to read many more from you!
I too own this set, and without a doubt I can say that it is the pride of my collection. After reading your remarks about how the proportions seem off, I compared the model to images of the real Y-Wing model and you were spot on, the engines do seem to be a bit too long and the cockpit too small in comparison. However, I took away the last section of each of the pylons and reattached the rear ends with the wheels with a handful of 2 stud-long technic axles, and... Well, do try it for yourself and tell me what you think of how it influences the overall proportions.