It flies! I had a mostly successful maiden flight this morning. Other than being a bit underpowered, it flies very nicely. It is able to slow down extremely well, but unfortunately it won't be breaking any speed records. It's a lot more agile than I expected and can actually turn pretty tightly, and it doesn't even bleed speed very badly in the turn. The landing gear servo was not strong enough to lift the gear against the force of the air, so I will be replacing it with a stronger one. With the flaps all the way deflected, the EDF is barely strong enough to keep it in the air on a 3s 1500 mAh pack, and even without the flaps I was full throttle the entire flight. On landing, I got a bit too slow, and the plane pitched up (it's an F-104 after all) and it came down from maybe 1.5 ft on its tail, but the only damage was it breaking the nose gear out of the retract and breaking the elevator bell crank, both of which I can fix pretty easily.
To fix the issue with it being underpowered, I am going to try flying it on a 4s 1300 mAh pack next time I get it out to the field. I did some bench testing, and the EDF should be fine with the 4s pack (it is rated to draw 38 A on 3s, but only draw about 25 A, even from a very large capacity pack with a high discharge rating, and it only draws 40 A max on 4s; I think they might have messed up and sent me the wrong EDF since it pretty closely matches the rated specs of the 4s EDF). Otherwise, now that I know it flies, I am going to go ahead and finish up the few remaining items and then paint it. One additional change I am going to make is to cut off the bottom of the fuselage where the skid plate will go and screw the skid plate in place so that I have an access hatch in case I need to change out servos or mess with the control linkages.