Complex WinMerge filters - otrs

Question

I've just started a project involving a customized OTRS 3.1.
In this project we have two folders, the original kernel folder, and the custom kernel folder.
If a file is present on the custom kernel folder, then it overrides the original kernel folder file. Thus, updating the version of OTRS 3.1 to the most stable one, is just a matter of substituting the original kernel folder. But We have a problem: if a customized file is updated, the update is ignored, since our customization overrides the original one. So we need to detect those conflicts in order to apply the enhancements to our customized file manually.
So to achieve it I planned the next strategy. Let's assume I have the next file at the original kernel file:
print "Hello ";
print "World\n";
I want to customize it, changing World by "ACME", So I copy this file to the custom folder and change it to:
print "Hello ";
##- CUSTOM CODE
##- Date: 10/02/2014
##- By: Dave
##- Original code:
=pod
print "World\n";
=cut
##< Start custom code
print "ACME\n";
## end custom code >##
=pod and =cut are a block comment
Now let's imagine that to print the word Hello is detected as a risk, and they change the code of the file on a new stable version to:
print "Hi ";
print "World\n";
When applying the change to my original folder, I will not take profit of the security fix, since I have a custom file that still contains the Hello word. That said, I want to use WinMerge (or other tool that can achieve the same result) to detect my custom code tags so:
The lines starting by ##- are ignored.
The lines =pod and =cut are ignored.
The blocks between ##< and >## are ignored
Thus the first original file and my custom file will be identical after filtered, but after the update, it will detect the difference and allow me to merge the changes to my custom version.
I know how to create the filter for the lines starting by ##- or equal to =pod or =cut. But I don't know how to ignore a multiline block from the comparison.
Do you know how can I achieve what I want? If not with WinMerge, Is there any another tool that can help me automating this task?
Thank you very much in advance!