Sorry, the wp post threw me for a loop. It appeared that you were trying to find wp paths within MODX, which you wouldn't ever find.
The two links on the home page, when you open the home page in MODX, are those links showing in the content area? If not, can you tell where they are coming from? They could be directly in the content, the template, or even from a chunk or tv. If you can find them, can you post the code?
In many cases (such as inserted with RTE), a link to a resource (page) in MODX will look like this (where [[~12]] is the ID of the resource being linked to):
<a href="[[~12]]">Link Text</a>
Although if the links are coming from say a TV, the [[~id]] part would use the MODX tag for [[*tvName]] or even simply be [[*tvName]] only as in the case of a TV set to the image type.
If your links are coming from absolute urls, often the path of the url will help you locate the page as it should resemble the structure of the document tree in the Resources tab. Find the parent, the child should exist within it.
Which website has another database? The MODX site or the WP site? MODX uses one single database, however you could have custom tables. How have you determined that another database exists?
Try the search in the MODX manager for your missing resources.