What alternatives exist, for your model, that can intercept serious supersonic threats and maintain a strategic advantage in VFR escorts that the F-35 cannot?
An F-104 would do the job, with modern avionics and engineering. If you want to guarantee bomber intercept capability, you have to be ready to tackle the nightmare scenario planes in the formation. The F-35 could intercept a Tu-95M with ease, but so could a F-16 or a F-117 armed with Sidewinders. You have to be capable of intercepting the real threats like the Tu-160 or Flanker strike formations, neither of which the F-35 can do much about.
An F-104 with modern avionics and engineering is an undefined, non-existent airplane.
Historically, there are few aircraft that fit that niche. (Mig-25, Mig-31, F-104 as you said etc). It would be cool to have a modern interceptor like that (F-15Ex with the pods, CFTs, and pylons removed??), but there's no existing solution that fits what you seek.
