I think that the problem is hard starting, no ignition on cylinder #4, and death when the throttle is opened. Is that correct?
If so, it tells me that there is a lean mixture, possibly combined with a bad wire on cylinder #4(changing spark plugs with #1 didn't change it). It's also possible that the Ignition Control Unit is having a problem resulting in a weak spark that can't handle the higher cylinder pressures when the throttle is cracked open.
What do we know for sure? Fuel pressure looks okay at approximately 35psi, valve clearance is good, injectors appear to be spraying, we have spark on cylinders 1,2,&3(possibly #4), and compression is good and balanced at 165psi on all cylinders. All the basics are there to make the engine run.
I don't recall seeing where the crankcase breather Z tube has been addressed. I would suggest looking there, as well as blocking the vacuum tube on the cylinder #4 throttle body. I base that on the report that the engine ran better when that throttle body was connected to the vacuum balancer.
If it were my bike, I'd be looking hard for an air leak.
It's also a very outside chance, but you might want to disconnect the throttle position switch. Sometimes it can cause a problem if it's faulty or maladjusted.