I have faf and supcom fa downloaded and have my faf linked to steam. But when I run the game through steam it's the vanilla steam version. I also can't play through the faf client either. I get this error 
Can't get supcom to work with faf
@slaple "when I run the game through steam it's the vanilla steam version"
Correct. Having FAF installed doesn't stop you from running the game through Steam. Even with FAF installed, when you run the game through Steam it will be the Steam version.
"I also can't play through the faf client either. I get this error"
I think your problem is that the FAF installation is in the "ProgramData" folder. I would suggest un-installing FAF, and then re-installing FAF to a different directory, such as "C:/Games/FAForever." You don't need to un-install FA (through Steam).
"The process cannot access the file because it is being used by another process"
- Restart your PC
- Start FAF without starting steam first.
I did both these things but trying to launch anything from faf come up with the error
java.util.concurrent.CompletionException: com.github.nocatch.NoCatchException: java.io.IOException: Cannot run program "C:\ProgramData\FAForever\bin\ForgedAlliance.exe" (in directory "C:\ProgramData\FAForever\bin"): CreateProcess error=2, The system cannot find the file specified
at java.base/java.util.concurrent.CompletableFuture.encodeThrowable(CompletableFuture.java:314)
at java.base/java.util.concurrent.CompletableFuture.completeThrowable(CompletableFuture.java:319)
at java.base/java.util.concurrent.CompletableFuture$UniAccept.tryFire(CompletableFuture.java:718)
at java.base/java.util.concurrent.CompletableFuture.postComplete(CompletableFuture.java:506)
at java.base/java.util.concurrent.CompletableFuture.complete(CompletableFuture.java:2137)
at com.faforever.client.fa.relay.ice.IceAdapterImpl.lambda$start$7(IceAdapterImpl.java:227)
at java.base/java.lang.Thread.run(Thread.java:832)
Caused by: com.github.nocatch.NoCatchException: java.io.IOException: Cannot run program "C:\ProgramData\FAForever\bin\ForgedAlliance.exe" (in directory "C:\ProgramData\FAForever\bin"): CreateProcess error=2, The system cannot find the file specified
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:64)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:500)
at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:481)
at com.github.nocatch.NoCatch.wrapException(NoCatch.java:61)
at com.github.nocatch.NoCatch.noCatch(NoCatch.java:104)
at com.github.nocatch.NoCatch.noCatch(NoCatch.java:82)
at com.faforever.client.game.GameService.lambda$startGame$39(GameService.java:637)
at java.base/java.util.concurrent.CompletableFuture$UniAccept.tryFire(CompletableFuture.java:714)
... 4 more
Caused by: java.io.IOException: Cannot run program "C:\ProgramData\FAForever\bin\ForgedAlliance.exe" (in directory "C:\ProgramData\FAForever\bin"): CreateProcess error=2, The system cannot find the file specified
at java.base/java.lang.ProcessBuilder.start(ProcessBuilder.java:1142)
at java.base/java.lang.ProcessBuilder.start(ProcessBuilder.java:1073)
at com.faforever.client.fa.ForgedAllianceService.launch(ForgedAllianceService.java:129)
at com.faforever.client.fa.ForgedAllianceService.startGame(ForgedAllianceService.java:74)
at com.faforever.client.game.GameService.lambda$startGame$38(GameService.java:637)
at com.github.nocatch.NoCatch.noCatch(NoCatch.java:100)
... 7 more
Caused by: java.io.IOException: CreateProcess error=2, The system cannot find the file specified
at java.base/java.lang.ProcessImpl.create(Native Method)
at java.base/java.lang.ProcessImpl.<init>(ProcessImpl.java:483)
at java.base/java.lang.ProcessImpl.start(ProcessImpl.java:158)
at java.base/java.lang.ProcessBuilder.start(ProcessBuilder.java:1109)
... 12 more
"C:\ProgramData\FAForever\bin\ForgedAlliance.exe" (in directory "C:\ProgramData\FAForever\bin"):
CreateProcess error=2, The system cannot find the file specified
looks like the (FAF) ForgedAlliance.exe is missing in C:\ProgramData\FAForever\bin\
- Please deinstall FAForever client.
- Delete the Folder
C:\ProgramData\FAForever\manually - Don't skip no 2. !
- reinstall FAForever (make sure your antivirus is off and not interfering with the download/install)
- Start FAF client and host a game
Because you did not post the full log i can't see if the ForgedAlliance.exe was downloaded from the client or not.
So from what i can see its maybe your antivirus programm that was deleting the ForgedAlliance.exe