Finally, I got working notepad.exe. I borrowed some lines from the GUI.script found in the latest MultiPE project. Insert the lines to the [Process] section of the GUI.script :
CopyOrExpand,%source_win%ADVAPI32.DLL,%target_sys%
CopyOrExpand,%source_win%APPHELP.DLL,%target_sys%
CopyOrExpand,%source_win%COMCTL32.DLL,%target_sys%
CopyOrExpand,%source_win%COMDLG32.DLL,%target_sys%
CopyOrExpand,%source_win%CRYPTUI.DLL,%target_sys%
CopyOrExpand,%source_win%DESK.CPL,%target_sys%
CopyOrExpand,%source_win%DISKCOPY.DLL,%target_sys%
CopyOrExpand,%source_win%IMM32.DLL,%target_sys%
CopyOrExpand,%source_win%IPHLPAPI.DLL,%target_sys%
CopyOrExpand,%source_win%KDCOM.DLL,%target_sys%
CopyOrExpand,%source_win%LSASRV.DLL,%target_sys%
CopyOrExpand,%source_win%LSASS.EXE,%target_sys%
CopyOrExpand,%source_win%MSGINA.DLL,%target_sys%
CopyOrExpand,%source_win%MSV1_0.DLL,%target_sys%
CopyOrExpand,%source_win%MSVCP60.DLL,%target_sys%
CopyOrExpand,%source_win%NCOBJAPI.DLL,%target_sys%
CopyOrExpand,%source_win%ODBC32.DLL,%target_sys%
CopyOrExpand,%source_win%OLE32.DLL,%target_sys%
CopyOrExpand,%source_win%OLEAUT32.DLL,%target_sys%
CopyOrExpand,%source_win%OLEDLG.DLL,%target_sys%
CopyOrExpand,%source_win%OLEPRO32.DLL,%target_sys%
CopyOrExpand,%source_win%POWRPROF.DLL,%target_sys%
CopyOrExpand,%source_win%RUNDLL32.EXE,%target_sys%
CopyOrExpand,%source_win%SERVICES.EXE,%target_sys%
CopyOrExpand,%source_win%SHELL32.DLL,%target_sys%
CopyOrExpand,%source_win%SHLWAPI.DLL,%target_sys%
CopyOrExpand,%source_win%SXS.DLL,%target_sys%
CopyOrExpand,%source_win%SYSSETUP.DLL,%target_sys%
CopyOrExpand,%source_win%UMPNPMGR.DLL,%target_sys%
CopyOrExpand,%source_win%URLMON.DLL,%target_sys%
CopyOrExpand,%source_win%USER32.DLL,%target_sys%
CopyOrExpand,%source_win%USP10.DLL,%target_sys%
CopyOrExpand,%source_win%VGA256.DLL,%target_sys%
CopyOrExpand,%source_win%WININET.DLL,%target_sys%
CopyOrExpand,%source_win%WINSPOOL.DRV,%target_sys%
CopyOrExpand,%source_win%WLDAP32.DLL,%target_sys%
CopyOrExpand,%source_win%WSOCK32.DLL,%target_sys%
I am sure there are some unnessary entries above but the quick test worked fine.