I'm a bit bit confused about the standards, like which nodes of which part should be deleted?
If I understand correctly, your goal has changed from the original post in this thread.
Your goal is to now to create a high quality mesh for your study area, right?
Perhaps if you list all of the things you know and all of the things you've tried then a modeller might help you fill the gaps and help you achieve your goal. But the first part is your homework; to carefully lay out what was done and what you understand so far. And what you think might be the problems that you're encountering.
Also, I'd suggest creating a new thread (with a nice subject closely aligned with your objective) rather than keep posting in this thread. That way, you may increase the likelihood that modellers (and others) will help you.
Kindly... Alan
PS Also sharing your t3m file may help people help you... but don't expect people to do your research for you...