3.0l Vulcan engine has a unique bell housing bolt pattern, so only a M5OD-R1 transmission from a 3.0l Vulcan will work, no there are no adapter plates.
And it also needs to match your drive line, i.e. 2 wheel drive or 4 wheel drive, if 4WD the transfer case from the auto will bolt up to manual 4WD trans.
Besides the transmission you really only need the Flywheel and clutch/brake pedal from another truck, you should get new clutch Master cylinder and clutch system regardless.
I think '95 to '05 clutch brake pedal assembly will work on the '99.
One problem you will have is that your computer has software to control an automatic transmission, and it probably has the PATS anti-theft system which is part of the computer software, that started to be added in 1999 V6 Rangers.
When you remove the automatic the computer will no longer have feed back from it, so it will turn on the CEL(check engine light) and it will stay on, forever.
While this is not the end of the world it does make passing emissions testing impossible, and if there ever is a real problem with the truck you won't know it because CEL is already on, you would have to check the codes all the time to see if any new ones have been added to the transmission codes.
There would also be some idle issues as the computer is running an automatic trans engine configuration.
Swapping to a 3.0l manual trans computer means you would have to swap out ignition key cylinder assuming you got the correct PATS keys with the new computer, or having a mobile locksmith with Ford software come out and add your current keys to new computer.
Computer must be in vehicle and working before new keys can be added, vehicle won't run until that has been done.
There are engine Computer programmers, that can tune computers for more power and better MPG depending on what you want, and they can often delete the PATS part of the software on some models, and they can also load Manual trans software deleting the current automatic software, but plan on spending $300-$400 at least.