1968 904 tranny filter, new does not match old one

Well I wish I would have know this 13 years ago when I put a deep pan kit on. The filter and extension only has one hole so the rear pump hole has been completelly blocked off. Trans has worked great until about 2 years ago. Has been out 3 times for the same thing. Pumping fluid out the front. Wonder if changing the filter to the correct one will help?