Its not going to be the fuse. The fuse also protects the receiver, IF, synth and logic sections of the radio and they're obviously working fine.
There could be a problem where power output may have been inhibited in software (either through deliberate settings in Programmer, or perhaps corruption of the tracking data). These should be easy to find with a bit of digging.
Or it could be a hardware problem, such as the directional coupler or antenna switch, or associated power control loop (the LPE has an incredibly fast PCL by the way). It could be the PA amps or preceeding buffers could be faulty. Perhaps the PA power control voltages, or the TX BPF tuning voltages from Attie are faulty. Or perhaps the I&Q mod from Jacqui is faulty.
What is the current draw on TX? If its about 1.5 ampere, you're in the ballpark and that would indicate the PA is doing its thing, and everything ahead of it.
Do you get any transmitted RF, even just leakage? Check on a service monitor or similar, holding the LPE close to, but not right at, the monitor antenna. If you're hearing something (with correct I&Q modulation) then you can eliminate Jacqui as being faulty.
Its all a process of elimination first, then go looking for specific problems in the areas you've narrowed it down to.