I have am having trouble getting the CVS to work with a custom SSH Port. How do I set up a custom port to be used for CVS through extssh?

I think it would be addressed to CVS guys, not us.
AFAIK, when ext protocol is selected, CVS runs whatever is pointed by CVS_RSH environment variable and there is no way to add arguments to have ssh connecting using non-standard port. CVS will run ssh with its own command line, embedded in CVS binary.

Okay. I thought I had done it in eclipse, however, when I went back and looked at it I noticed they use :extssh: which allows the port number after the ipaddress: and before the cvs repository location (ie :extssh: mylogin@192.168.1.1:2022/mycvs/repository.) I guess it doesn't work with :ext:. Apparently there is a way to define the default ssh port in a config file but I can only find instructions for linux config files and not windows.

Thank you anyway. If I can't get this to work I will have to look for debugging tools else where.

you can select "Custom" in the protocol selection dropdown and enter :extssh: mylogin@192.168.1.1:2022/mycvs/repository in the CVSRoot input.

I did try that. For some reason it didn't work. I am not sure what "tools" are needed for it. I finally got the ssh to work on a different port. I downloaded openSSH and dropped a config file with PORT = 2022 in my windows user folder. That now allows it to connect on port 2022 without a problem; however, it is not passing the password.

The cvs waiting box comes up and just sits there with the status bar moving up to about 90% and then it waits. When I cancel it I get an error message that says, Please input password. I have a password in the password field in the set up for CVS so I am not sure why it isn't getting passed. I am currently working setting up a public/private key combination so that may take care of it.

Right, public/private keys are way to go.
But did you replace our cvs.exe with your own?
Our would not hang.
Also please check what cvs.exe and ssh.exe are pointed by in the tools->settings->tools

When I went to tools there was no ssh.exe selected. When I searched for an ssh.exe there wasn't one installed so I installed openSSH. If that was incorrect then where is your ssh.exe located?

I did not replace your cvs.exe. I left it as it was installed.

Right. We do not distribute any ssh tools with PhpED. Mostly due to licensing problems.
Feel free to install openssh as a part of cygwin.
Then locate ssh_config in /etc and specify port you need to be used by ssh.
Other ssh distro may fail to run password dialog as they may not support calling askpass for this.