A few formatting comments:

I think qq and combined statements are clearer here:

    if ($shpath) {    
      #print SH "chmod 700 $shpath/shell_$ts.sh\n";
      #print SH "$shpath/shell_$ts.sh\n";
      #print SH "rm $shpath/shell_$ts.sh\n";
      #push @cmd, "pscp -pw \"${passwd}\" \"${shell}\" ${user}\@${serv
+er}:${shpath}/shell_$ts.sh\n";
      #push @cmd, "plink -batch -pw \"${passwd}\" ${user}\@${server} -
+m \"${sh}\" >> \"${output}\" 2>${outerr}\n";
      print SH "chmod 700 $shpath/shell_$ts.sh\n",
               "$shpath/shell_$ts.sh\n",
               "rm $shpath/shell_$ts.sh\n";
      push @cmd, qq[pscp -pw "${passwd}" "${shell}" ${user}\@${server}
+:${shpath}/shell_$ts.sh\n],
                 qq[plink -batch -pw "${passwd}" ${user}\@${server} -m
+ "${sh}" >> "${output}" 2>${outerr}\n];
    } else {
      ...
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You have many "if it begins with X, trim off X" cases that can be simplified:

      #if ($sqlline =~ /^=/) {        # Convert the output to record v
+iew if prefixed by =
      #  $sqlline =~ s/^=//;          # trim off the =
      if ($sqlline =~ s/^=//) {       # trim off '=' and convert recor
+d view if prefixed by =
        $rsql = 1;
      }
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And maybe:

    #$server   =~ s/\s+.*//;
    #$user     =~ s/\s+.*//;
    #$passwd   =~ s/\s+.*//;
    #$dbconn   =~ s/\s+.*//;
    #$dbuser   =~ s/\s+.*//;
    #$dbpasswd =~ s/\s+.*//;
    #$shpath   =~ s/\s+.*// if $shpath;
    map{$_ && s/\s.*//} $server,$user,$passwd,$dbconn,$dbuser,$dbpassw
+d,$shpath;
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