Ok the solution which worked for me is in two parts:
Writing .aff file by your own is a pretty lengthy and difficult task. So if you want to create your own custom dictionary(provided it is not very complex and deep in lexical terms) just create an empty file in notepad and save it with .aff extension, it will work fine.
I came through this problem because I wanted to merge two different Hunspell Dictionaries with their .aff and .dic files. And I found a brilliant FREE Hunspell Merge tool which can merge Hunspell Dictionaries (both .aff and .dic files) generating combined .aff and .dic files.