Did you solve your problem?
I have to copy the DB from 2005 and insert it to a 2008r2 server. Then I export the DB from 2008r2 to the 2000 server so I can run the perl script. After the perl script runs then I bring the DB back to its orginal 2005 server.
That sounds like a lot of work. I can understand why you might want to avoid it. Are these copies exact copies, or are you transoforming the data somehow?
I presume you have tried running your script directly against the SQL Server 2005 database instance. If you do, what happens? Does the script produce an error message? If so, what is it?