Connectivity timeout between cluster nodes I lose communication between my clusters almost 1 am to 1.30 am and it shows errors like 35206 on primary, 976 on clusters, sometimes the cluster is removed due to lost heartbeat leading to 1135 error , 1069 error. I have a strong feeling that my connection breaks everyday at that time but im clueless where to start kind of lost. any help will be greatly appreciated.
Have you checked SQL error logs? Start with what the description of errors. Is it because it lost quorum? Is there high CPU in any of the nodes? Are you on FCI or AAG?

We had to adjust timeout between our replicas when the databases were reporting unhealthy during high peak ETL loads. 

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Set up trace to investogate what other things are running on the server. Then check SQL wait stats. https://www.sqlskills.com/blogs/paul/wait-statistics-or-please-tell-me-where-it-hurts/

If there is no load - increase your timeout to a higher value (https://blogs.msdn.microsoft.com/alwaysonpro/2014/06/03/connection-timeouts-in-multi-subnet-availability-group/)) and see if the errors go away. However, if you have no problems in your workload then you should not worry about these errors. First you need to assess if users are complaining of slowness, are there any jobs failing during this time? You have to ask these questions before trying to simply reposlve an error.