1. Is news.php the default page,
Yes
if I upload index.html will it be the default page as with most servers?
I'm afraid not. But one of the things coming in the very near future is an "Advanced Layout Options" for the news page, so you can completely customize your news page accordingly.
2. Are there any limits on .js files, I am planning to use adobe spry for a few 'enhancements'.
Nope.
3. The default tool-tip, I saw no css to adjust its appearance.
There are a few default tool tips in the system. Which one are you talking about in particular.
I have many more questions, but I will hold off for now. The template is still a work in-progress so to speak. Then there is integration to your system.
I'm ready when you are