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so, 986 5- and 6-speeds, and 987 5- and 6-speeds, will all bolt up. not sure about the 987 units, but 986 5- and 6-speed transmissions have different input shafts requiring different clutches (and probably pressure plates, fasteners, etc., while you are in there). transmission mounts should be the same, but the brackets differ. reverse switch plugs are different, as are clutch slave cylinders and lines. most likely you have to change exhaust mounting hardware, and shift cables are specific to each transmission.
the real work is with the axles. there are differences in length, flanges at the transmission, and wheel bearings/carriers. i can't recall, but 986 6-speed transmission axles require beefier bearings that may not fit into the 5-speed uprights? can't remember, but check parts catalogs to determine diameters, splines, etc., for fitment.
as far as what to choose, size=strength with transmissions. the 987 6-speeds are actually smaller than the 986 6-speeds, so you may wish to consider a 986 6-speed. cheaper and easier to find as well.
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