I know the answer to your first part of the question. The cockpit can be moved around by editing the Server.lua file in the Config/view folder. Just remember to that every update will revert this back to a default file so you will have to re-edit this every update. I haven't tinkered around with makeing the autoconfig on this part yet so I dont know if and how to do it.
As for inputs, try making your entry.lua part look like this instead: "make_flyable('Mirage 2000-5', current_mod_path..'/Cockpit/KneeboardRight/', nil, current_mod_path..'/Comm/Mirage2000-5.lua')" I cant say that will work because I dont have your folder stucture on some things, but that might help. If not, you might want to double check everything over name spelling wise to make sure it all matches up. If you dont mind posting what you have or PMing me I can try and take a look for you.