this code is doing many things ... couldnt debug what mistake i am doing

These two statements are not unrelated. There are various aspects of your code as it stands which will hinder debugging. The main one is that it is monolithic - if you were to split out the various parts into subs it would help to isolate problems and allow for simpler testing.

Other potential pitfalls include:

• Inconsistent indenting. perltidy is an obvious tool to help with that.
• Lack of fault tolerance. eg. calling chdir without checking to see whether or not it has succeeded. Consider autodie as a first-order fix.
• Lack of meaningful comments. Some lines of code commented out with no explanation as to why.
• Variables assigned to which are never read (eg. $filesynth). perlcritic can pick up such situations.

Writing quality code isn't easy but having put the effort in (even just using the tools I've mentioned) it does make debugging, testing and maintenance so much easier.

Good luck with your ongoing debugging.