So, I can take this license from each of the physical ESXi 4.1 machines and get a free pass to 6.0?
If your subscription is active (or was active at the time when ESXi 6.0 went GA) you will be able to upgrade the license. Simply log in to your MY VMware portal, go to the licensing section and select Upgrade License Keys from the drop down list. If the Essentials Plus 4 keys show up, you are entitled upgrade them.
I downloaded the standalone converter, but still not aware how to thin it out.
I'd suggest you setup the new environment and then run VMware Converter to do a V2V (virtual to virtual), i.e. converting from the old to the new environment. VMware Converter allows you to select an advanced mode for the disk migration where you can select the target virtual disk size.
André