Little unclear as to what you are asking... maybe a little background might help?
The 999 was a 'heavy duty' 904 found behind 360 equipped cars and trucks. The only difference between a garden-variety 904 and a 998/999 is the amount of clutches in the drums. After 1978, the 999 was a 'lockup trans' in which the lockup function was controlled hydraulically. People confuse lockup for overdrive but the 999 is the same as any other Torqueflite with a 1:1 high gear, maybe a few hundred rpm difference at cruise. Lockup basically just keeps the converter from slipping.
As fr as identifying what you have, Sedanman is correct in that the input shaft on a lockup is different than non - the non is splined all the way to the tip. The front pumps are different, that is for sure. Unfortunately, there were enough variations over the years that it can be hard to mix and match parts and get what you want. The PK # on the driver's side pan rail will help identify the unit though the only real way to know what's inside is to open it up and determine how many clutches are in the drums. Externally they all look the same from the '60s-'80s.
As for the non-lockup VB in a lockup trans - it would probably work on some level but there may be some things that don't match up. If that's what you have going on now, then you know the answer is no. I believe there are some differences between non lockup and lockup valve bodies but don't quote me on that. Again, lockup was controlled by the hydraulic system and was related to road speed/load so there would almost have to be some differences in the valve body for the lockup function to work.
A manual valve body will work as long as it's for the correct application. I have a factory non lockup 999 with a an older Turbo Action forward manual valve body, works great. If you are looking to buy a manual valve body, then it would help to know what trans you have. Again, unless you built it yourself, the only way to know if you have an A999 is to take it apart.
If you don't want to deal with any of that jive, just use the early 904 and be done with it. They respond to modifications just like any other transmission, build it however you want. Again, all Torqueflites have a 1:1 high gear so your highway rpms will be about the same regardless of which unit you have. If you are using a manual valve body, lockup is pretty much out the equation anyway.
