There are certainly ways to improve the performance of the plane, but the problem with doing too much, especially if you're talking about swapping away from radial engines or other clearly visible modifications is that it becomes too easy to distinguish visually from the B-17s and the Luftwaffe fighters just don't engage them. The whole point of the concept (as I understood, anyway) was that an unsuspecting interceptor would think they were attacking a regular Fortress until it was too late and they suddenly found themselves staring down far too many .50 cal barrels. If a pilot can ID the YB-40 from outside of machine gun range then it's a trick that will only work until the Luftwaffe figure out that they don't have bombs and can be ignored.