SP2010 : Custom Site Template in Publishing site

Hi,

I am having a publishing site template where I have sub-sites being created based on a custom Site Template (contains Pages, Custom Visual Web Parts, 2 SP2010 Groups).

I have the following issues,

1. When I create a new sub-site using the save Site Template, the custom Master Page does not get attached to the new sub-site automatically. I have to Manually go change it every time. This is tedious when you have several sub-sites which have to follow the same sub-site template look and feel approach. Any suggestions why this is happening and how I can fix it?
2. All the custom web-parts added to the Site Template pages are missing in the newly created sub-site's respective pages, where I then need to go and manually add the web-parts and configure them.  Strange thing is the Default page (Welcome Page) has all the web-parts (CQWP, VWP,etc) which I added in the custom Site Template but all the other Pages does not. Why is this happening and how can I solve it?
3. I have two SP2010 groups in the Custom Site Template (CommiteeAdmin & CommitteeMembers). This is used to check which AD user is assigned to the particular group so that I can handle the permissions through code in my visual web-part. But for some reason I cannot access these two groups through code. Only way I can access is to create a new group with a unique name for each sub-site I am creating. 

I feel the above issues defeats the purpose of the Custom Site Template. Am I doing something wrong?

Best Rgds,

SSP

SSP