The Paper Size and Header/Footers will only change if there are section breaks included in what you are bringing across. So you can clean the content by deleting section breaks before the transfer to avoid that issue. The Style list reset is repaired by refreshing the styles from the Normal template.
Try this version of the macro
Code:
Sub CopyPasteToTemplate()
Dim InputDoc As Word.Document, OutputDoc As Word.Document, i As Integer
Set InputDoc = ActiveDocument
Set OutputDoc = Documents.Add 'Normal template by default
'remove section breaks from input, replace with a hard page break
With InputDoc.Range.Find
.ClearFormatting
.Replacement.ClearFormatting
.Text = "^b"
.Replacement.Text = "^m"
.Wrap = wdFindContinue
.Execute Replace:=wdReplaceAll
End With
'make autonumbers and bullets hardcoded
InputDoc.ConvertNumbersToText (wdNumberAllNumbers)
'Make graphics inline, skip errors
On Error Resume Next
For i = InputDoc.Shapes.Count To 1 Step -1
InputDoc.Shapes(i).ConvertToInlineShape
Next i
On Error GoTo 0
'remove formatting from input
With InputDoc.Range
.Style = wdStyleNormal
.ParagraphFormat.Reset
.Font.Reset
OutputDoc.Range.FormattedText = .FormattedText 'bring content into new doc
End With
OutputDoc.UpdateStyles 'restore style settings in output from Normal template
OutputDoc.Activate
End Sub