Here's an idea for getting their attention (worked for me) - I found the right person's name, bought an AdWords campaign with his name as the keywords. And then emailed him just one sentence "when was the last time you googled your name"? with a link to google search his name.
A. No one can resist something like that. B. The ad linked to the unique cover letter (unindexed, so they won't see the other ones:) and that linked to the resume. C. Total cost was like 5 bucks because he showed it to ~10 people - def. worth it.
The bottom line is - anything that will get the right person's attention would do :)
I am not suggesting this is the best way to go for a development position. But the principle is the same - you have to stand out.
Each of your questions requires a pretty lengthy discussion that can rarely be covered in a forum but I've addressed the above question at length in an old blog post of mine: http://voltsteve.blogspot.co.uk/2011/09/how-to-find-job-for-...
If you're UK based then have a look through our site: http://www.hackerjobs.co.uk