Make the border on one bar darker than the others

I haven't got your data so I have used the diamonds dataset to demonstrate.

Basically you need to 'overplot' a second geom_bar() call, where you filter the data= attribute to only draw the bars you want to highlight. Just filter the original data to exclude anything you don't want. e.g below we replot the subset diamonds[(diamonds$clarity=="SI2"),]

d <- ggplot(diamonds) +  geom_bar(aes(clarity, fill=color))    # first plot
d + geom_bar(data=diamonds[(diamonds$clarity=="SI2"),],        # filter
aes(clarity), alpha=0, size=1, color="black") +                # plot outline only
  facet_wrap(~ cut) 

NB obviously your filter will be more complicated, e.g.

data=yourdata[(yourdata$visualcondition=="LeftCust" & yourdata$report=="Left" |
                 yourdata$visualcondition=="SIMCust" & yourdata$report=="SIM" |
                yourdata$visualcondition=="RightCust" & yourdata$report=="Right"),]

OK updated with your data. I had to make up confidence intervals because they weren't available in the AggBar2 data:

######### ADD THIS LINE TO CREATE THE HIGHLIGHT SUBSET
HighlightData<-AggBar2[AggBar2$Report==gsub("Cust","",AggBar2$Visual),]
#####################################################

prob.bar = ggplot(AggBar2, aes(x = Report, y = Prob, fill = Report)) + theme_bw() + facet_grid(Audio~Visual)
prob.bar + geom_bar(position=position_dodge(.9), stat="identity", colour="black") + theme(legend.position = "none") + labs(x="Report", y="Probability of Report") + scale_fill_grey() +

######### ADD THIS LINE TO CREATE THE HIGHLIGHT SUBSET
  geom_bar(data=HighlightData, position=position_dodge(.9), stat="identity", colour="pink",size=1) +
######################################################

  labs(title = expression("Visual Condition")) +
  theme(plot.title = element_text(size = rel(1)))+
  geom_errorbar(aes(ymin=Prob-ci, ymax=Prob+ci),
                width=.2, # Width of the error bars
                position=position_dodge(.9))+
  theme(plot.title = element_text(size = rel(1.5)))+
  scale_y_continuous(limits = c(0, 100), breaks = (seq(0,100,by = 10)))

Similar to Troy's answer, but rather than creating a layer of invisible bars, you can use the size aesthetic and scale_size_manual:

require(ggplot2)
data(diamonds)

diamonds$choose = factor(diamonds$clarity == "SI1")

ggplot(diamonds) + 
  geom_bar(aes(x = clarity, fill=clarity, size=choose), color="black") +
  scale_size_manual(values=c(0.5, 1), guide = "none") +
  facet_wrap(~ cut)

Which produces the following plot: