## Some sample data
set.seed(0)
x <- rexp(100, 1/5)

## Default boxplot
boxplot(x)
abline(h=quantile(x, probs=c(0.02, 0.98)), col="blue", lty=2)  # add your quantiles

## Copy the function and change the stat-calculating part of its body
mybox <- boxplot.default
body(mybox)[[10]] <- quote(
    for (i in 1L:n) {
        bstats <- boxplot.stats(unclass(groups[[i]]), range)
        bstats$stats[c(1,5)] <- quantile(unclass(groups[[i]]), probs=c(0.02, 0.98))
        groups[i] <- list(bstats)
    }
)

## Now, use it and compare
mybox(x)
abline(h=quantile(x, probs=c(0.02, 0.98)), col="blue", lty=2)  # add your quantiles