I have mine set to 50,000 and 1,000.  The default settings are too low for us.  I doubt it affects performance much. 

And do you have a full backup & uninterrupted transaction log backups from before the problem occured ?

Sorry, I haven't used merge replication.

I haven't tried that. If you add the index at the publisher, you'll probably have to add it manually at the subscriber if you don't want to re-snapshot.

 I did this with good results when I needed to change the length of a field in a replicated table. -- Specifically: Drop a table from a publication...

Sounds as though someone deleted it from the subscriber table ... a "no-no".

You could re-initialize .... basically start over. To find the row, you have to run a "diff" between...

Disable the Delete function.  Assuming you're on 2000, go into the publication properties, then articles. Click the box to the right of the article, then pick the "Commands" tab. Uncheck...

No.  What I mean is, if you are using snapshot replication, then you can change the column length at the publisher. Then, the next time snapshot replication runs, it will...

If it's only used in snapshot replication, I'm pretty sure you can just change the published table, and it will get pushed to the subscriber next time it runs.

I've changed the retention period for a case when we only replicated data every 2 weeks or so.

I haven't used merge, but with trans repl, I do this:

Script out the "drop publication" commands

Paste into QA, and find just the portion that applies to the specific table. sp_drop_article...

But I think if you modify the DTS package at a later date, it reverts back to the original owner.

I have some notes that I ran this script to change...

I've only given SQL Safe a quick lookover, so I don't know the answers. 

Do you want the results of the query in the subject line ?

Yes, the primary key exists in the Subscriber table. Replication needs the PK in order to retrieve the subscription records to apply the replicated transactions.  You do have other options...