I agree, I would separate initial cloning (better use plain rsync) and 
backup operations (a case for backuppc). From what you wrote, I am not 
even sure whether - once you have done the initial cloning - in steady 
state you want to do "backup" (periodically take incremental or full 
snapshots) or "synchronising" (make sure that file-system zones 
correspond to each other - again, simpler to do with plain rsync).

For cloning, you could consider preparing a filter file for rsync, 
probably using a simple script that collects file- and directory names 
you want / do not want to transfer and that already formats them into 
the format needed by an rsync filter file, and maybe than manually 
review these contents to catch specific cases. If you write a filter 
file, the sequence is important (to distinguish catching file abc and 
file abcd).

The -t option of rsync makes it preserve the modification time, and the 
-c option tells rsync to use checksum (does it use md4?) or size+mtime 
to decide whether files are identical. And yes, handling of links is a 
little bit messy to set up correctly.

Rsync is complex, idem the man-page. In case you want examples of 
command lines and filter files to get a quick start, say so.

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