I converted my 3-speed Saginaw to a Muncie and used the original bellhousing, clutch linkage, and tranny crossmember. I upgraded the flywheel and clutch, but I think cam67 is correct, the Muncie should be a direct swap.
While you have everything apart, I would replace the clutch fork pivot ball that screws into the bellhousing. Mine was worn pretty bad. Replace the clutch fork if there's any wear on the end. A new clutch means a new throw-out bearing. Also, the tranny mount usually gets covered in oil, which weakens the rubber. Replacements are cheap.
Oh - the speedo cable screws into a Muncie on the passenger side. It goes in on the driver's side on a Saginaw. You will need a new speedo cable and will have to drill a new hole in the firewall to run the cable through. Hole placement can be determined with the factory engineering diagrams. The book is available from most resto shops.