Just because an index is clustered doesn't necessarily mean it is the best index to use. If you store a large amount of data in the tables, especially if you use varchar(max), text, or image data types, then you should probably create another nonclustered index on the joining identifiers. A clustered index will cover blob data and make the row seeking perform very slowly.
You should run the sprocs as TSQL and have the SQL Server Management Studio output an execution plan. CTLR+M = "Display actual execution plan" then save the execution plan, upload it, and i'll take a look at it.
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