No, the next chapter is not almost finished. Unfortunately, at this point we are no longer even certain whether episode 4 will be finished this year (although I still hope we can achieve this).
As for using the ships in Secret Ops, you have to include files not just from the /ships folder, but also from /mesh and /mat. If the game is telling you that there is a file missing, it's also telling you which file is missing - just read the error notice and you'll work out the problem.