Jon Richard wrote:

I've asked on another board and this is a 1/2 ton pick up, but there were enough mustang's running these transmissions I figured someone here may know.

Realizing there are modern 5 speed options I'd still like entertain hot rodding the little original 3 speed in my truck with a gear vendors.

Does anyone know if the input and output shafts and tailshaft housings are interchangeable between a 3.03 3 speed and a Ford design top loader 4 speed?

Don't know about your truck, but the top loader was a direct replacement for the original 3-speed in my Mustang.  The only major change was to the speedo cable.  The top loader has it on the right side while the 3 speed has it on the left side.
 

Truck three speed transmissions have the really short tail shaft and rear housing.  If you go with the longer Mustang style toploader, you will need to change the tranny mount and driveshaft length.  Also longer speedo cable for the four speed and the reverse helix driven gear for the cable. Four speed cable is on passenger side requiring longer cable. Note the cable routing under the dash and across the firewall floor are different for the four speed.
I do not know if the tail shafts and housing interchange between the 3 and 4 speed.  There are some good truck forums out there.  And a lot of experts on what interchanges, same as you find with Mustang info on FYIFORD.