Hi looks like you can change TransmittalSetups by just adding the corrects bytes to file or to make much life much easier just use a simple subsitution cipher to decode it to a xml file.
Here is part of the sheet set file that comes with autocad samples you will see transmittal setups at bottom.
I will post code for converting soon but pretty easy figure out mapping since you modify the sheet set file see results.
Here is a start
http://www.theswamp.org/index.php?topic=46497.0
<?xmlversion="1.0"encoding="UTF-8"?>
<AcSmDatabaseclsid="g2162C6B6-0CE4-40E8-912B-46F59DFDF826"ID="gA9DFEA28-A450-4076-8C0F-6ABA0418E5FF">
<AcSmProppropname="DbFingerPrint"vt="8">g89B8180B-4DB0-4C97-974E-01F9483859B8</AcSmProp>
<AcSmProppropname="DbVersion"vt="8">1.1</AcSmProp>
<AcSmProppropname="FileRevision"vt="3">36</AcSmProp>
<AcSmSheetSetclsid="gB20534F2-0978-418C-8D14-2E6928A077ED"ID="g50786B62-0394-4DC2-B91D-3790BAB7A345"propname="SheetSet"vt="13">
<AcSmFileReferenceclsid="g6BF87AE7-1BEC-4BDB-98BB-5B91F7772793"ID="gC9C96A82-979D-4EA0-B827-97B8D27C0B06"propname="AltPageSetups"vt="13">
<AcSmProppropname="Environ_FileName"vt="8">%ProgramFiles%\AutoCAD 2006\Sample\Sheet Sets\Architectural\IRD.dwt</AcSmProp>
<AcSmProppropname="FileName"vt="8">C:\Program Files\AutoCAD 2006\Sample\Sheet Sets\Architectural\IRD.dwt</AcSmProp>
<AcSmProppropname="Relative_FileName"vt="8">.\IRD.dwt</AcSmProp>
<AcSmProppropname="SpecialFolder_FileName"vt="8">$(CSIDL_PROGRAM_FILES)\AutoCAD 2006\Sample\Sheet Sets\Architectural\IRD.dwt</AcSmProp>
</AcSmFileReference>
<AcSmCalloutBlocksclsid="g203EAB46-483B-4E6B-A10B-15E9A4B210FF"ID="g3D8FB2D2-42BE-408B-9DC8-59C4B2DF4142"propname="CalloutBlocks"vt="13">
<AcSmAcDbBlockRecordReferenceclsid="g11782523-474B-4C83-9646-57C052847FBB"ID="g82BD5C32-9E78-4A1D-A4D4-8F5AE4FAC610">
<AcSmProppropname="AcDbHandle"vt="8">25C04</AcSmProp>
<AcSmProppropname="Environ_FileName"vt="8">%ProgramFiles%\AutoCAD 2006\Sample\Sheet Sets\Architectural\IRD.dwt</AcSmProp>
<AcSmProppropname="FileName"vt="8">C:\Program Files\AutoCAD 2006\Sample\Sheet Sets\Architectural\IRD.dwt</AcSmProp>
<AcSmProppropname="Name"vt="8">Callout Bubble</AcSmProp>
<AcSmProppropname="Relative_FileName"vt="8">.\IRD.dwt</AcSmProp>
<AcSmProppropname="SpecialFolder_FileName"vt="8">$(CSIDL_PROGRAM_FILES)\AutoCAD 2006\Sample\Sheet Sets\Architectural\IRD.dwt</AcSmProp>
</AcSmAcDbBlockRecordReference>
.......
...........
<AcSmCustomPropertyValueclsid="g8D22A2A4-1777-4D78-84CC-69EF741FE954"ID="gE16F3C7B-AA0F-4BDB-B7DB-FD7655411FDC"propname="TransmittalSetups"vt="13">
<SSTransmittalSetups.16clsid="g087CF7BD-9343-4946-8BEE-44578710527E"ID="gCA88A6E5-F97C-41CC-8450-76CCA4B03351"propname="Value"vt="13">
<SSTransmittalSetup.16clsid="gFEBD61A0-4DCA-4CC1-A461-6801ED213209"ID="gD3E48FF3-5A43-49A5-BE47-F8CB680AB2F3">
<AcSmProppropname="IncludeDataLinkFile"vt="3">1</AcSmProp>
<AcSmProppropname="IncludeMaterialTextures"vt="3">1</AcSmProp>
<AcSmProppropname="IncludePhotometricWebFile"vt="3">1</AcSmProp>
<AcSmProppropname="IncludeSSFiles"vt="3">1</AcSmProp>
<AcSmProppropname="SetupName"vt="8">Standard</AcSmProp>
<AcSmProppropname="VisualFidelity"vt="3">1</AcSmProp>
</SSTransmittalSetup.16>
<SSTransmittalSetup.16clsid="gFEBD61A0-4DCA-4CC1-A461-6801ED213209"ID="g0B4A5B1A-F80D-4DB3-8FCE-FF3721CEB693">
<AcSmProppropname="IncludeDataLinkFile"vt="3">1</AcSmProp>
<AcSmProppropname="IncludeMaterialTextures"vt="3">1</AcSmProp>
<AcSmProppropname="IncludePhotometricWebFile"vt="3">1</AcSmProp>
<AcSmProppropname="IncludeSSFiles"vt="3">1</AcSmProp>
<AcSmProppropname="IncludeUnloadedReferences"vt="3">1</AcSmProp>
<AcSmProppropname="SetupName"vt="8">ArchiveStandard</AcSmProp>
<AcSmProppropname="VisualFidelity"vt="3">1</AcSmProp>
</SSTransmittalSetup.16>
</SSTransmittalSetups.16>
</AcSmCustomPropertyValue>
</AcSmCustomPropertyBag>
You can also find your answers @
TheSwamp