Please look at this link to old site because I am not able to post in new site due to error "Sorry new user can not mention more that 2 users in post". Not sure what that means. Moderators can help on that I hope. Thank you
Please consider formating your sql - makes it so much easier to read (it was really a bracked hell to get thru).
As to optimizing your where section, not much to do:
WHERE (@CUSparam = 113
OR dbo.E_Estimates.Customer = @CUSparam
)
AND ((@CHKparam = 0
AND dbo.E_Estimates.[Assy Q] = -1
AND dbo.E_Estimates.E_Status IN (1,2)
)
OR (@CHKparam = -1
AND dbo.E_Estimates.[Assy Q] IN (-1,-2)
))
AND ((@FLDparam = '[Part Number]'
AND dbo.[Part Numbers].PartNumber LIKE '%' + @TXTparam + '%'
)
OR (@FLDparam = '[Description]'
AND dbo.[Part Numbers].[Description] LIKE '%' + @TXTparam + '%'
))
You should look at placing correct indexes on your tables, to gain performance.