This isn't a direct answer to your question, but since you said, "Think F-104", maybe it will give you some insight. A lot of years ago, I worked for a flight test organization which had, among other planes, 5 F-104's. Part of what I did was perform weight and balance calculations whenever we did modifications to these airplanes. I don't recall the exact numbers, but it seems like the acceptable CG range was from -7% to about +12%. MINUS 7%? Yep, that's right. The CG was ahead of the leading edge of the wing. From that you might surmise that the fuselage (and intakes) had a huge affect of the airplane's aerodynamic center.

Dick