Having direct access shouldn't be an issue but if your server is in like New York and you are using a database in Seattle which is where our webhosting is, then yes that could be a problem.
Only way to fix that problem is to upgrade to a unmanaged VDS or use a MYsql lite plugin.
Can Mysql be installed on the VDS, and if so, which versions are supported and what is the best way to install it?
You should be able to use the latest version and yes it can be installed on an unmanaged VDS. As for the best way I am not sure. There are surely some guides floating around. I would do a quick Google search to see.
NFO currently provides the hourly backup for our current server, but as I understand, backups will be my responsibility on a VDS. Any suggestions on how best to handle this?
There are multiple plugins for Bukkit which will take server backups whenever you choose. Some might cause lag, others might not. Depending how active you are it might even be better to just logon ever hour or so..etc and create a backup.
With the current bundle, we have the 50 slots on 2GB of ram. Is the 2GB VDS comparable, or do I need to up to the 3?
It's hard to compare a MC server to a VDS server as all MC servers are run off of specially picked machines with a lot of ram and SSD. There is also some overhead from the virtual environment for a VDS which can loose a little bit of performance. Personally I would test it out and see how it goes.
Should I anticipate needing to pre-purchase additional bandwidth, or would I be fine with the monthly allotment?
You should be fine with the allotted bandwidth for each plan.
We have a Ventrillo server with NFO, will this need to be installed or is this still a seperate server?
Voice servers are not able to be hosted on managed machine and you need to a license to run anything over 8 slots for Ventrilo. You can keep your existing Ventrilo through by doing a change order.
Am I barking up the wrong tree to begin with? Is there a better way to go about doing this?
In all honest I would try to experiment around with some other plugins that do the same thing and see if you can get it working correctly. As the performance we offer on our MC machine is very high and sometimes hard to match. Upgrading to a VDS, especially an unmanaged one is a big step and has caused problems for some people, while others have experienced no issues at all. It all depends on what you are needing. Like I said, think about it for couple of days, talk it over with your community and get some ideas before you proceed.