LITP,
There were six different top tunnel inspection covers made for the 40 Series and those included a 3-speed cover and a cover for PTO installations.
From 10/82 four of those remained.
The four speeds used a flat cover; the five speeds needed the additional height of the raised cover.
There are two 4-speed inspection covers. The general use four speed cover(58262-90084) that started in 1/79 was "modified" in 10/82 with a different part number(58261-90800); however, for some strange reason the earlier version continued to 4/86 for Venezuela-spec trucks only--unsure just why this is so.
I have only seen one version of the raised cover(58261-90801), and I believe it to be intended for the five speeds. However, I do have an '83 longbed that came with a raised cover for its 4-speed and cannot see any differences between that cover and a known 5-speed cover. It fits snugly and the shifters and boots seem correctly positioned. With all the intervening years and previous owners, it could be a factory-installed 5-speed cover, or a swapped out 5-speed cover, OR.....perhaps it is the 10/82 up four-speed cover(58261-90800) which might be raised--I wouldn't know if I saw one. It appears to exactly match the other 5-speed covers I have, but since the covers are not part-stamped, cannot determine. The rubber "packing" gaskets for the covers DO have part numbers, but I'm too lazy to remove this cover and check its gasket for a number. In any event, the truck is happy using this cover with its 4-speed transmission, so I'm guessing that the raised covers can be also used for the 4-speeds without modification.
The 45 series pickups apparently never received the 5-speeds, and with the various versions of the floor stampings out there, it is odd that a 5-speed cover would fit the 45 series pickup tunnel, unless the 5-speed tunnels have the same footprint configuration as the 4-speed tunnels, at least in the area of the inspection covers. I suspect the tunnels for all 40-Series are all the same after 10/82 and include the RH lower bump-out into the RH("passenger") floor area.
My understanding is that you also plan to install a 5-speed into a 1964-1967 pickup LPB? If so, the earlier tunnels may possibly be not shaped exactly as the 1/79 up tunnels where you need to install the inspection cover, so some fabrication might be indicated for this type of install. If this is your plan, have you dry-fit a 5-speed cover over your existing tunnel near where you'll need it?
BTW, along with the inspection cover gasket, the outer boot for the transmission shifter, and both the inner and outer boots for the transfer shifter changed on the raised covers from the 1/79-10/82 ones more commonly seen. All or some of these boots and the gasket may be long discontinued.