Your initAllApplication should be be like this, as you have two application System1 and SHAOnline so here you are initializing both of them done.
Then in Your Main.xaml workflow after the IF first run, you have to invoke 3 workflows as per below.
In the Process.xaml workflow have to invoke 4 workflows as per the screenshot
In System1 Extract Work Item Data Table workflow after extracting the table assign WIList to ExtractDataTable.Select(“Type=‘WI5’ AND Status=‘Open’”)
And the way your direction in WIList were was fine the one in System1 Extract Work Item is Out and the one in GetTransactionData direction is ‘in’
Hope this will be helpful