I wanted a single script to do the lot

With the unix tools installed on all machines, you could have a single script on a single machine that does something like this:

my $find = "find /path -type f -print0 | xargs -0 md5"
for my $host ( @hostlist ) {
    open O ">$host.md5list" or die "$host.md5list: $!";
    print O `ssh $host '$find'`;
    close O;
}

# compare lists here, if you like, or use a separate script/tool to do
+ that
[download]

That assumes that you have the appropriate authentication keys for using ssh without a password to connect to each host. Other methods are possible for the connections, of course.

(updated the script to include "xargs -0", and to run the md5 part on the remote host, where it belongs -- note the single quotes around $find in the ssh command line.)

(another update: I should confess that I have no clue how you would actually execute a shell script on a remote windows machine... good luck with that.)