You should do a clean installation of Domino 5.0.7a on your new server, and then move the data from your old server. Before turning Domino on, you should Compact -B the databases. Then run Fixup on them and then run Updall -R. This will bring all of your databases in R5 ODS, which is fine. R4.x client can access R5 ODS (ODS 41) databases as long as they are on a R5 server.
Dig deeper on Domino Resources - Part 7
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