Watch the process of one of the clients to see what is pulling all the resources.
When you replicate, it needs to check for all changes since last replication. On large dbs this can take some time. Then it needs to update view indexes and full text indexes.
Does this occur only the first time in the day or each time it replicates?
Also remember that every email sent is replicated twice, once in the mail file and once as a send mail.