Hopefully you have already got it sorted out.But if you haven't let me give you a suggestion:
Look at Post number 1 on this thread by Pier39lab.Download the form.Get attested copies of all the documents and send it to them on the address provided by Pier39lab.It is very likely that you will get a letter stating all the procedures that you
haven't followed and that need to be followed.Don't forget the logbook pages and the demand draft.It could take a couple of months for them to reply.
I don't know the exact procedure myself, but I'm reasonably sure that the above indirect method would work.They normally reply back and list the reasons why your application has been denied.
There is no need to panic.If you want to sort out this mess you are going to have to be patient.
Hopefully someone else here is able to guide you more precisely.