Best practices for deploying a large application to a new environment for the first time?

Hi all, we're looking to deploy our application of about 3,000+ objects to a new environment for the first time. We've split the application into 3 smaller applications, one which contains the DB objects, one which contains the groups, and the last one which contains the rest. 

I'm going to look at deploying the DB changes, then the DB objects, groups, and lastly the rest of the application. My main concern is dealing with timeouts - when we've tried to deploy a lot of objects in the past (using compare and deploy) we've seen an issue where the deployment takes so long that it eventually times out. Is there any way we can split the objects further to deploy them in smaller batches?

Any other advice would also be appreciated.

Thanks.

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