I tried asking on the tridef forums but go no response.

Is there a guide to the manual focus settings? I'm trying tridef with FSX and the autofocus doesn't seem to work well. Clouds have a lot of separation but closer objects have zero separation (like the control stick on the cockpit) - which is the opposite of how things should be (anything inside the cockpit area is practically 2D).

Does anyone have any pointers on manually adjusting these settings?

First read MANUAL about tridef 3d ignition, and second do it like this if you need more advanced afto-focus:

"If you really want to modify a DDD profile, you can go to the profile folder, make copy of that profile and rename (DDD) to (Username). This new profile is now modifiable in game. It is considered a hack that we do not officially support."

After that just run ignition with game u need, push 0 (open OSD) than u find "PROFILE"....and do it whatever u want