I don't see any reason for keeping directories and files separated, as you are mapping one file to each directory in a one-to-one correspondence. You could create two arrays and then access the items as you like, but I think a simpler and straightforward way for doing this could be just creating a list of files including the full path. You could loop through your list of files like this:

#!/usr/xpg4/bin/sh
#
#
MAINDIR=/apps/main1
FILECOMP=/apps/scripts/rename.txt
SCPINFO=box1:/path/to/location

theFilesList='Test1/Ready/file1.csv Test2/Ready/file2.csv Test3_Part3/Ready/file3.csv ....'

umask -S
# Dates the log file
echo "" >>$LOGDIR 2>&1
`/usr/bin/date >>$LOGDIR 2>&1`

# ------- START PROCESSING ---------
for i in $theFilesList
do
FNAMETMP=/usr/bin/find . -name *.txt -newer $FILECOMP 2>>$LOGDIR
# Rename
mv $FNAMETMP $i 2>>$LOGDIR
# Move to archive
mv $FNAMETMP archive 2>>$LOGDIR
# SCP to another server
scp $i $SCPINFO 2>>$LOGDIR
# Update the File for comparison
touch $FILECOMP
done
exit


If you are interested in using arrays, then you can define two arrays like:
set -A theDirectories Test1/Ready Test2/Ready ....
set -A theFiles file1.csv file2.csv ...

To access an array element:
${Directories[_position_of_the_item]}

To loop through an array:
for i in ${theFiles[@]}
do
echo $theFiles
done

To get the number of elements:
${#theFiles[@]}

That is using the Korn Shell though...