Checked out files will remain checked out to that user. Created By/Modified By will remain until you migrate that content via a content migration tool, such as Sharegate. Otherwise if you perform database attach upgrades, the data will remain consistent.
The ID which gets from Get-SPServiceApplication command is the ID of the "Usage and Health Data Collection Service Application".
The second ID is the ID of Usage and Health Data Collection proxy. This is the proxy that virtualizes the access to the service application.
Opened falls under the view type of the audit type enumeration:
It is different to check-in/check out. From what I remember viewing encompasses download and opening with client or owa, but not viewing properties (but I am not 100% sure on the last one).
Add a new SharePoint 2013 server (must be SharePoint 2013 w/ SP1 ISO, then update to your current patch level), add it to the farm, start Service Instances as appropriate, then remove your old server from the farm.
Those are the basic steps to swap out a SharePoint server.
This is correct behavior. Columns are defined at the site collection level or list level so deleting a subsite will not delete them unless they were defined as list columns.
You need to go to site settings on the parent site collection --> Site columns and then delete them from there.