On our front page we have a Module showing the latest videos but when you click on one the popup is messed up.

You have to use scrollbars to see the video. Is there a way to make this so the video and the popup have no scrollbars?

Here is the link:
kyhorsepark.com/test2/

Did you try increasing the lightbox height and width offset values on the module settings?
If you have tried that and it doesn't work, check if a file named "component.php" exists in your active joomla template directory.
If it doesn't, you have to create it (see Joomla forums how to do it).
If it does exist, you need to edit it or its css to achieve the results you need. Note that any changes will affect all other joomla components as well.

This seems to have got me going on the right path. I am still having trouble reducing the player size in the lightbox popup player.

www.kyhorsepark.com/test2
Click video at bottom of page.

I don't think your lightbox is working. You have javascript errors. Search the forum on how to fix them. Moreover, you should turn off Videoflow's mootools legacy mode on the configuration panel.