cd RAR

echo "Getting RAR files from North Server"
wget -q ftp://username:password@xxx.xxx.xxx.xxx/*.rar;type=i
echo "Getting RAR files from South Server"
wget -q ftp://username:password@xxx.xxx.xxx.xxx/*.rar;type=i

echo "Unpacking RAR files"
unrar -o+ -inul e *raw

echo "Removing .rar files"
rm *.rar

echo "Renaming files and moving them to directories by type"
for src in *;
do
    type=$(echo $src | sed -e "s/^.*_//" | sed -e "s/.report//")
    tgt=$(echo $src | sed -e "s/\(^.*\)\.\(.*_.*\)/\2/")
    echo "Moving $src to ../$type/$tgt"
    mv $src ../$type/$tgt
done

cd ../CRS

echo "Processing CRS files"
for src in *.report;
do
    # Set some variables
    type=$(echo $src | sed -e "s/^........//" | sed -e "s/\(^...\).*/\
+1/")
    dest=$(echo $src | sed -e "s/report/csv/")
    tid=$(echo $src | sed -e "s/_.*$//")
    echo "Src= $src"
    echo "Type=$type"
    echo "Dest=$dest"
    echo "TID= $tid"
    echo ""

    # Check to see if this is a Flashwave
    if   [ $type = "FOS" ] \
      || [ $type = "FOT" ] \
      || [ $type = "FOU" ] ;
    then

        # If it is a Flashwave...
        echo "This is a flashwave"
        cat $src                    |
        sed -e "/FILL,0,$/d" > /tmp/sedtemp

    else

        # If this is NOT a Flashwave...
        echo "This is NOT a flashwave"
        cat $src                    |
        sed -e "/FILL,0,$/d"        |
        sed -n "/,[1-2][,-].*,$/ {
            h
            N
            s/^.*,\(.*\),$/\1/
            H
            x
            s/\n//g
            p
        }
        /,[0-9]\{1,2\}.*,$/ p" > /tmp/sedtemp

    fi

    # Find  each Port ID section and duplicate it using , instead of -
    cat /tmp/sedtemp    |
    uniq                |
    # Special case - no dash in Port ID, just a single number
    #sed -e 's/\(,[0-9]\{1,2\}\)$/\1,,,,,/'              |
    # Cleanup caused by special case
    #sed -e 's/,,,,,\([0-9]\{1,2\}\)$/,,,,\1,,,,,/'      |
    # Special case - no dash in Port ID, just a single number
    sed -e 's/\(,[0-9]\{1,2\}\),$/\1,,,,,/'              |
    # Main Port ID reformat
    sed -e 's/,\([0-9]\{0,2\}\)-\([0-9]\{0,2\}\)-\{,1\}\([0-9]\{0,2\}\
+)-\{,1\}\([0-9]\{0,2\}\)-\{,1\}\([0-9]\{0,2\}\)/,\1-\2-\3-\4-\
5-,\1,\2,\3,\4,\5/g'   |
    # Delete mulitple dashes
    sed -e 's/--/-/g'   |
    # Do it again just to make sure
    sed -e 's/--/-/g'   |
    # Delete trailing dashes
    sed -e 's/-,/,/g' > $dest

    # Update the tidlist
    echo "Updating tidlist"
    echo $tid >> ../tidlist.txt
    echo ""

done
[download]

Things like this:

tid=$(echo $src | sed -e "s/_.*$//")
[download]

I would change to this:

tid=${src%%_*}
[download]

Often the 'echo ... | sed ...' lines can be replaced with shell parameter expansion, which can speed up some scripts. Overall though, I don't know if it'll do much for you. Your big sed pipe could be put into one sed command, and your deletion of multiple dashes looks wrong (especially since you do it twice), do you want this?: s/--*/-/g. And as merlyn might point out, you have a few useless uses of cat. You could use either input redirection or specify the file on the first command. In keeping with your current style, this works in ksh, I don't know about bash:

<file \
sed s/this/that/g
[download]

There are cases when sed is faster than perl, and the other way around. Last time I compared, it seemed that when I used alot of character classes (e.g., [0-9], etc.) perl tended to be faster. Update: or maybe when I could replace things like [0-9] in sed with \d in perl, and needed case insensitive matches, which you can't do with the old standard sed.