I have had several Tokheim 39's and never seen a rubber gasket used between the top and side panels. No reason it wouldn't work and there are several supplies that sell "U" channeled rubber window gasket that should do the job.
There should be a small gap between the top and side panels and Speedracer's suggestion about using a washer might help but the carriage bolts that hold the top down need to fit(lock in to) in the bracket welded under the front of the top.
I am currently putting two short 39's together that use hinged doors and one has the brackets and one does not. Can't tell if they both did and one set was simply removed or never installed.
