1) I have not, so can offer no useful advice here.
2) I have typically set a "dummy" domain and password just because, but that may be overkill and pointless configuration. Open to other ideas on this question.
Not to get basic on you, but remember that your current VLAN databases/configuration is tied to your VTP domain, so when you start configuring from server/client to transparent mode you're going to start losing VLAN configs in devices. Depending on the size of your network and criticality, this may not be a trivial issue.
3) Private VLANs are a method of keeping ports in the same VLAN, but restricting traffic between those ports. An example would be a set of servers (say mail, DNS, web) that are on the same subnet, in the same VLAN, but you ONLY want those servers to have access to the Internet, and NOT each other. The servers could be on the same private VLAN with an Internet port set as the promiscuous port. The servers could talk to the promiscuous port, but not each other. I would recommend the Guest VLAN as its own vlan (no devices other than guest devices), thus negating the need for the private VLAN. But to answer your question, the "gateway" port would be the promiscuous port. You'll find a plethora of information on the Cisco site, but here is one starting point:
http://www.cisco.com/en/US/tech/tk389/tk814/technologies_configuration_example09186a008017acad.shtml
Good luck!
Ed