If you have time to learn a little bit of R programming language you can use ggplot2 library to add confidence interval to your scatter plot. Here is an example showing correlation of horse power with miles per gallon

library(ggplot2) 

ggplot(mtcars, aes(x=hp, y=mpg)) + 
  geom_point() + 
  geom_smooth(method="lm") + 
  theme_classic()

Are you positive the reviewer means to add error bars to the correlation plot? I think he means to add error bars to the qPCR bar plot on the right since these measurements are done in triplicates and you have error. Also, you should present the validation plot as qPCR as a bar plot with error bars and the RNA-seq as a line plot, or vice versa. This can be easily done in excel which you used already. This being said, I'm assuming you do not have replicates for the RNA-seq analysis. Hope this helps.

As mentioned above you want x and y error bars, which corresponds to the fold-change expression on that axis. So, the x direction error bars correspond to the rna-seq values and y direction to the qPCR values. So there is no need to collapse anything. This is quite simple to do. See the error bar tab/section for the plot in excel. You can even highlight the cells that have the error values to use for each point and its direction.