This is totally untested, but I'd suggest a way to simply filter the "." out of the username. Looking at a freshly downloaded version of the MOD, try the following changes.
outputFile.asp (line 74)
membername = Replace(UploadRequest.Item("memberName").Item("Value"),".","")
myfiles.asp (line 144)
FileNamePath = Left(Server.mappath(Request.ServerVariables("PATH_INFO")),pathEnd) & "\" & strUploadUrl & "\" & Replace(strDBNTUserName,".","") & "\" & Name
myfiles.asp (line 169)
FileNamePath = strForumUrl & strUploadUrl & "/" & Replace(strDBNTUserName,".","") & "/" & Name
myfiles.asp (line 218)
Path = Left(Server.mappath(Request.ServerVariables("PATH_INFO")),pathEnd) & strUploadUrl & "\" & Replace(strDBNTUserName,".","") & "\"
Do the same with the Select Case for extensions from lines 315-422.
I think those are all the changes you'd need to make. You might have to tweak it a bit, since I threw this together in about ten minutes, but it should at least get you going.