Based on my understanding of what you have stated, we might use FSO and then grab files with same name. Then check for their file extension and proceed with comparison. This would be two conditional checks.
So what ever files are available in both the folders would only go in for a comparison, all others in either folder would just be ignored.
I am not sure, if this helps but this is again based on my understanding!!
Here is a quick function that returns an array with the files inside a folder. You can collect arrays of the contents of each folder and then compare the two. It sounds like you also need to search them for a list of files that must be present, and another list of files that should never be present.
Dim fso, f, fl, sf
Set fso = CreateObject("Scripting.FileSystemObject")
Set f = fso.GetFolder(folderspec)
Set sf = f.Files
i = 0
For Each fl in sf
fl_len = len(fl)
fs_len = len(folderspec) + 1
new_fl = right(fl,(fl_len - fs_len))
ReDim preserve File_list(i)
File_list(i) = new_fl
i = i +1
CheckFolderFiles = File_list