Ok, I have made some progress with the use of the find command combined with a tar pipe to copy symlinks preserved as they would be first before cp command would copy over as links all other files without overwriting the links that were already correctly copied over. The find and tar pipe takes .75 seconds to copy over all 21,000+ symlinks in my 1.8GB main SCE. That SCE takes a better part of a minute to load normally, more or less I have not timed it, so there is almost no performance penalty.
This should solve a LOT of errors like we have seen and prevent the use of starup scripts to have to copy over individual broken or wrong symlinks as we find them. This method would be advantageous for Core as well, since symlinks should be copied as is to the live file system and not a symlink created pointing to a symlink buried in the mounted /tmp/tcloop area.
Hopefully I will be able to wrap this up and upload the results tonight.