Why you think it could be a problem?
I believe using shared connections for long time should not cause timeout error, unless there's a connectivity problem or a dba has set some connection time.
If the database server is strong enough to hold the large processing data then do not be scared and these days they are usually strong. I do use several jobs to share connections and they pull/push large volumes of data without any connection time out issue.
If you still are scared of the job might see a failure because the connection is open then try not using share connection, but instead local connection contexts to component and the output component you can see in the Advanced settings, "commit every" and "batch size" properties.
Also did you try using tHashInput and tHastOutput to check if they will increase the speed? They do for me.
Also it depends on how you are running the job, via the client or the server TAC or exporting to some unix server. They have varying effects.
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