Replication to server with different Port

I have a SQL server running on a remote location that has a different port
enabled to connect other than the default one, which means that when I want
to register I have to specify the port number as well eg.
Server1\InstanceName,4001 .
I am trying to carry out merge replication between the server and the MSDE
on my box. I have set up the pubisher, registered the SQL Server from
Enterprise Manager on my machine and on setting up the subscriber I am able
to view the publication in the list of registered servers. Creating the
subscription works fine, but when I try to sync , I get the error 'The
process could not connect to Distributor 'Server1\InstanceName' . I feel that
this is because of the port since it is not mentioned in the message and SQL
is trying to use the default port. Is there some workaround for this?
.

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