I don't know what saddle you're using. Obviously, mine are Brooks'. They work best for most people when tilted slightly up. The original saddle on that Specialized road bike in the first pic was a Milano. Cheap, but decent out to about 40 miles. It usually feels best when level. Whatever saddle you use is really immaterial for now. You just need to get comfortable with what you have, right?

As far as breaking loose that stuck stem: You can turn the bike over and spray WD-40 inside the head tube to soak the tapered wedge and get it to soak the stem quill. In the end, it might take a good whacking to bust it loose. Just make sure you hit it square-on, not a glancing blow.

A bar that is 3cm lower than the saddle would bother me after about 15 miles. Good luck.