Use awk to help convert fixed width to csv. Not tested extensively. Works based on stacks of spaces at common positions.

fwf2csv.R

fwf2csv <- function(infile) {
  if (infile == "clipboard") {
    infile <- tempfile()
    writeLines(overflow:::readClip(), infile)
  }
  
  a <- tempfile()
  text <- 'BEGIN{ FS=OFS=""; ARGV[ARGC]=ARGV[ARGC-1]; ARGC++ }
NR==FNR {
    for (i=1;i<=NF;i++) {
        if ($i == " ") {
            space[i]
        }
        else {
            nonSpace[i]
        }
    }
    next
}
FNR==1 {
    for (i in nonSpace) {
        delete space[i]
    }
}
{
    for (i in space) {
        $i = ","
    }
    gsub(/,+/,",")
    print
}'
  writeLines(text, a)
  command <- sprintf("awk -f %s %s", a, infile)
  system(command, intern = TRUE)
}

http://stackoverflow.com/a/30869273/1270695