If I understand your question correctly, continue building the new 5.5 environment with your 3 hosts from scratch "ignoring" your old hosts. Once your new environment is up & running, connect the 4.1 hosts to your new vCenter Server and use vMotion to move the VMs while they're running to the new cluster (live migration with no downtime).
VMTools upgrades do not take place automatically during migrations.
Once your VMs are on the new hosts, update the tools as your normally would and you can then also upgrade the virtual hardware of your virtual machines.
Virtual HW upgrade is optional, though; if you don't have VMs that need the new features you can skip this last step and keep them as they are.