I am suggesting that when you create the data connection in your InfoPath form template, you include the Where clause by clicking the Edit SQL button in the data connection dialog that generally shows the SQL data structure tree. Set the data connection to not run on load.
Then save your form as source files (from the Publish backstage).
Then open manifest.xsf in a text editor and look for your "Where" clause - remove that from the SQL in manifest.xsf. Save your changes. Right click manifest.xsf and select Design. This opens the form in design mode. Use File > Save As to pack your form back up as an XSN.
Now, you should be able to use the qRules ModifySQL command to add a new, dynamic Where clause to your query as needed.
Does that make sense?
To directly answer your question about the timeout - I do not know of a way to adjust the time out for a data connection while walking through the data connection wizard. Once the connection has been created, the timeout can be adjusted via qRules or code.