Can you try this and see what takes the longest?

I'm guessing it's the FT search. Maybe if it gets narrowed down before doing that it will help somehow.

declare @tbl1 table (id bigint primary key)

declare @tbl2 table (id bigint primary key)

declare @tbl3 table (id bigint primary key)

insert into @tbl1

SELECT AuditLogID

FROM AuditLog

WHERE (CreatedDate between '9/18/2012' and '9/21/2012')

AND (CustomerID = 2046 and PracticeID = 1)

--print time

insert into @tbl2 select auditlogid from

@tbl1 t inner join

auditlog a on a.auditlogid = t.id

where

CONTAINS(([ChangeSet], [EntityTypeText], [SubEntityTypeText], [UserName]), 'Eduvigis')

--print time

insert into @tbl3 select auditlogid from auditlog where

@tbl1 t inner join

auditlog a on a.auditlogid = t.id

where

CONTAINS(([ChangeSet], [EntityTypeText], [SubEntityTypeText], [UserName]), 'Phillips')

--print time

SELECT AuditLogID, Application, AuditActionTypeID, AuditTypeID, ChangeSet, EntityTypeID, EntityTypeText, SubEntityTypeID, SubEntityTypeText, CustomerID, PracticeID, UserID, UserName, CreatedDate

from @tbl2 t inner join

AuditLog a on a.auditlogid = t.id

ORDER BY CreatedDate desc

--print time

SELECT AuditLogID, Application, AuditActionTypeID, AuditTypeID, ChangeSet, EntityTypeID, EntityTypeText, SubEntityTypeID, SubEntityTypeText, CustomerID, PracticeID, UserID, UserName, CreatedDate

from @tbl3 t inner join

AuditLog a on a.auditlogid = t.id

ORDER BY CreatedDate desc

--print time