That seems a pretty fair summary of the problems, now what are the answers? 
My guess is that RWB didn't share all of what he had found out with his off-spring. I think that where CAE and later DB shared RWB's distrust, suspicion and disdain for JB, they were not made privy to some of the info he received.
I think JB had a dodgy side which impacted upon some but not others. Those who he impacted upon had no qualms about getting shot of him and subsequently stuck together when the need arose (i.e. statements / scratches / silencer). I think the financial implications regarding estate / inheritance etc, merely compounded the fate of JB. However I have a feeling that in the case of RWB, there was more to it than that, i.e. it was more of a motivation. I think that after the killings, everything JB had ever done or said was reinterpreted with a sinister bent.
I think the police were stuck between a rock and a hard place due to the raid / crime scene etc. Under mounting pressure, they chose the lesser of two evils from their own perspective. They burned a cad and they twisted arms / called in favours to do so. It was slight of hand. They ruthlessly ditched anything that was supportive of JB, in order to play up the cad. The silencer evidence was created and the whole Mugford episode was engineered, coerced and managed, literally micro managed. It must have been an exhausting process to make her 'credible'.
I think potential waverers were silenced in the wake of Taff Jones' death. If there was nothing sinister in it, they had still lost their figurehead. It was a new regime.
In two months time, I'll probably tell you something completely different.