When launched wizard sees the Sharepoint Website as IIS 7/7.5 web

This is a know issue that is very easy to miss. Usual indication
is if the web parts do not appear after deployment.

It usually means that the user used to launch the wizard
does not have the access to the SharePoint database, so it’s recommended to use
the same user account that was SharePoint deployed to be used for Web Server
deployment.

When crawling content sources times out with: "The filter daemon did not respond within the timeout limit"

This issue is fixable by increasing the timeout value in SharePoint:

http://technet.microsoft.com/en-us/library/ee808862.aspx

When crawling content sources fails with: Error while crawling LOB contents. (Access denied by Business Data Connectivity. )

This could be related to SharePoint app pool user change after the installation was already accomplished.
This can be changed by manually changing BDC object access rights to a required
user.