When you run an installation rather than an upgrade, you need to configure the host (networking etc.) and then re-add the VM's to the inventory by right clicking the .vmx files on the Datastore Browser. There's no need to install ESXi on a different storage (e.g. flash drive), you can interactively install ESXi on the host (preserving the VMFS datastores), which will overwrite the previous ESXi installation and start with default settings.
André