> -- Recreate the unique index<br>
> CREATE UNIQUE NONCLUSTERED INDEX IX_tblManifestDetailsFWC_NaturalKey<br>
> ON dbo.tblManifestDetailsFWC (ManifestLineID ASC, FederalWasteCode ASC);
What I don't see here is an index on FederalWasteCode, so your lookup "where FederalWasteCode = 'K061') is not using this index. You can prove that by running the query in SSMS (bypassing for a moment any smarts that LINQ might add) and turning on the Execution Plan.
Mind you, an index on ManifestLineID is important for joining with the parent table, but you need an additional index.