Could Try This

#Create your md5 file based on a path - recursively
pathtocheck=INSERTYOURPATHHERE
find $pathtocheck -type f -print0 | xargs -0 md5sum >> xdirfiles.md5

#Compare All Files
md5results=$(md5sum -c xdirfiles.md5)

#Find files failing Integrity Check
echo "$md5results" | grep -v OK

#Count the files good or bad.
lines=0
goodfiles=0
badfiles=0
while read -r line;
do
  lines=$(($lines + 1))
  if [[ $line == *"OK"* ]]; then
    goodfiles=$(($goodfiles + 1))
  else
    badfiles=$(($badfiles + 1))
  fi
done <<< "$md5results"
echo "Total Files:$lines Good:$goodfiles - Bad: $badfiles"

That's for your own play up there... to directly answer your question on how to make it check for dir2... simply force the /dir2/ in front of each file w/ sed. It gives an absolute path to check the file.

sed -I "s/  /  \/dir2\//g" xdirfiles.md5

[root@server testdir]# md5sum somefile
d41d8cd98f00b204e9800998ecf8427e  somefile
[root@server testdir]# md5sum somefile > somefile.md5
[root@server testdir]# sed -i "s/  /  \/dir2\//g" somefile.md5
d41d8cd98f00b204e9800998ecf8427e  /dir2/somefile

breakdown of the sed command used

sed -i <- Inline replacement.
s/ <- Means to substitute. (s/thingtoreplace/replacewiththis/1)
"  " <- represented a double space search.
/ <- to begin the Replacement String values
"  \/dir2\/" <-  Double Spaces and \ for escape characters to use /. The
final /g means global replacement or ALL occurrences. 
/g <- Means to replace globally - All findings in the file. In this case, the md5 checksum file seperates the hashes with filenames using a doublespace. If you used /# as a number you would only replace the number of occurrences specified.

The most basic form of operating would have one copy the checksum file made from running:

md5sum Dir1/* 

over to the directory you are wanting to test validity of the copying done. (If you do this while also copying the other files when your backing up or the likes, then you don't have to do it separately with:)

cp checksum Dir2/checksum
cd Dir2

Changing to the second directory can make commanding things simpler, and if your likely to have to deal with missing files it will help assure you have the proper path to the files working in the terminal (and its history of commands) which can, if nothing else, let one copy and paste them into the command lines later.

md5sum -c checksum 

Gives the integrity of that copied.