Pentesting 3000 hosts in details is way too much, even for a team.
Since time is money and the ultimate goal of a pentest is to make your organization more secured, you have to target specific hosts and go from there.
For example, take a few representative workstations, find the vulnerabilities, fix all 2000 workstations (if required), then try again to confirm things are better now. Also, scan for specific services (like port 80 and 443 for web servers) that shouldn't be opened on workstations. You can also check network traffic for odd things and go from there.
For the servers, again go after typical basic installation, start with the ones containing sensitive data or thoses exposed to the internet, etc. You want to make sure that the critical servers are secured first, then move to less critical ones. You will also find that if a server has a vulnerability, chances are that other servers have the same problem and training is required.
So I could go on and on about this, but there is no way you can spend, let's say, half a day on each host. Because after 1500 days of work (With about only 220 working days in the year, assuming you work alone), the first host you would have scanned 6 years ago would probably be vulnerable by now...

So you have to be smart about it...