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Perhaps there are better ways to solve it, but it works if you use ctrl-d instead.
Please use code-tags instead, and use indenting in your code for better readability.

Don't know if I understand the problem exactly, but this sed maybe solve it:
sed -E 's/([^~]*~){18}3?/&\
/'

I think some of the suggestions posted before mine will solve your problem, but if you want to know why var=$(echo $var|tr -d '\n\r')isn't working it's that you must use double quotes: var=$(echo...

I don't have so much to say about using "\" more than it's an escape for the following newline character, like esacping e.g. "$" with "\$". So perhaps it's important that there is no character (space...

You forgot "$"
DATE3=(perl -e '@f=localtime(time-(86400*7));printf "%02d%02d%02d\n",$f[5]%100,$f[4]+1,$f[3];')should be
DATE3=$(perl -e '@f=localtime(time-(86400*7));printf...

If you have FreeBSD try
date -v-7d +"%y%m%d"Adjust the format to what you want.

should be:

/usr/local/bds/mailsend.s mailx "Backup Default Data File has been used"
<email address> <email address> /export/home/tjmoore/de
fault_data_backup_email 2>&1...

I still haven't studied your script in details, and don't understand what you mean with "hard time in that CP command", but there is one more thing I noticed:
...
SubmitBatchJob () {
max=$2...

for line in $(cat data1)...using for x in... is using values delimited by space, not newline, if you want to use your code as it is you must change the delimiter to newline:
EDIT: IFS seems to be...

Shouldn't you have backticks in the for-line?
for BackupFile in `ssh -q oracle@${RHOST} ${CCMD}`; do

I think "&&" is the logical "AND", "||" means "OR", so it should be
command || echo "error occurred"

in the first example
[[ $@ =~ [^0-9 ] ]] # (double "[[") means if any character is not a digit or blank
In your second example you forgot "then"

or use grep with "-e"
grep -e "--"