SSIS Package runs for 500x longer on one server

Question 1

If you have logging turned on, preferably to SQL Server, add the OnPipelineRowsSent event. You can then determine where it is spending all of its time. See this post Your IO subsystem getting slammed and generating all these temp files is because you are no longer able to keep all the information in memory (due to your async transformations).

The relevant query from the linked article is the following. It looks at events in the sysdtslog90 (SQL Server 2008+ users substitute sysssislog) and performs some time analysis on them.

;
WITH PACKAGE_START AS
(
    SELECT DISTINCT
        Source
    ,   ExecutionID
    ,   Row_Number() Over (Order By StartTime) As RunNumber
    FROM
        dbo.sysdtslog90 AS L
    WHERE
        L.event = 'PackageStart'
)
, EVENTS AS
(
    SELECT
        SourceID
    ,   ExecutionID
    ,   StartTime
    ,   EndTime
    ,   Left(SubString(message, CharIndex(':', message, CharIndex(':', message, CharIndex(':', message, CharIndex(':', message, 56) + 1) + 1) + 1) + 2, Len(message)), CharIndex(':', SubString(message, CharIndex(':', message, CharIndex(':', message, CharIndex(':', message, CharIndex(':', message, 56) + 1) + 1) + 1) + 2, Len(message)) ) - 2) As DataFlowSource
    ,   Cast(Right(message, CharIndex(':', Reverse(message)) - 2) As int) As RecordCount
    FROM
        dbo.sysdtslog90 AS L
    WHERE
        L.event = 'OnPipelineRowsSent'
)
, FANCY_EVENTS AS
(
    SELECT
        SourceID
    ,   ExecutionID
    ,   DataFlowSource
    ,   Sum(RecordCount) RecordCount
    ,   Min(StartTime) StartTime
    ,   (
            Cast(Sum(RecordCount) as real) /
            Case
                When DateDiff(ms, Min(StartTime), Max(EndTime)) = 0
                    Then 1
                Else DateDiff(ms, Min(StartTime), Max(EndTime))
            End
        ) * 1000 As RecordsPerSec
    FROM
        EVENTS DF_Events
    GROUP BY
        SourceID
    ,   ExecutionID
    ,   DataFlowSource
)
SELECT
    'Run ' + Cast(RunNumber As varchar) As RunName
,   S.Source
,   DF.DataFlowSource
,   DF.RecordCount
,   DF.RecordsPerSec
,   Min(S.StartTime) StartTime
,   Max(S.EndTime) EndTime
,   DateDiff(ms, Min(S.StartTime)
,   Max(S.EndTime)) Duration
FROM
    dbo.sysdtslog90 AS S
    INNER JOIN
        PACKAGE_START P
        ON S.ExecutionID = P.ExecutionID
    LEFT OUTER JOIN
        FANCY_EVENTS DF
        ON S.SourceID = DF.SourceID
        AND S.ExecutionID = DF.ExecutionID
WHERE
    S.message <> 'Validating'
GROUP BY
    RunNumber
,   S.Source
,   DataFlowSource
,   RecordCount
,   DF.StartTime
,   RecordsPerSec
,   Case When S.Source = P.Source Then 1 Else 0 End
ORDER BY
    RunNumber
,   Case When S.Source = P.Source Then 1 Else 0 End Desc

, DF.StartTime , Min(S.StartTime);

You were able to use this query to discern that the Merge Join component was the lagging component. Why it performs differently between the two servers, I can't say at this point.

If you have the ability to create a table in your destination system, you could modify your process to have two 2 data flows (and eliminate the costly async components).

The first data flow would take the Flat file and Derived columns and land that into a staging table.
You then have an Execute SQL Task fire off to handle the Get Min Date + Delete logic.
Then you have your second data flow querying from your staging table and snapping it right into your destination.

Question 2

The steps below will help improve your SSIS performance.

Ensure connection managers are all set toDelayValidation ( = True).
Ensure that ValidateExternalMetadata is set to false
DefaultBufferMaxRows and DefaultBufferSize to correspond to the table's row sizes
Use query hints wherever possible http://technet.microsoft.com/en-us/library/ms181714.aspx

SSIS Package runs for 500x longer on one server

Appendix A

Notes