Welcome to iBoats.
Prepare yourself ? psychologically - for this project to turn into a full restoration. Boats rot from stern to bow and from the bottom up. If the deck is rotted, everything below (Stringers and bulkheads,?.) is questionable to say the least and if the front is rotted, the transom is also questionable.
I know this is not what you want to hear, it wasn?t what I wanted to hear when I was in your shoes, but it is the truth nonetheless.
You need to take some core samples of the transom and stringers. What setup you have, I/O or outboard? How is the engine perform, did you take a compression test and inspect it mechanically?
Take a look at few Bayliner complete restoration projects in the full restoration forum here
http://forums.iboats.com/forum/boat-repair-and-restoration/completed-boat-projects
Just search for Bayliner and you will get so many of them. Any questions, just ask away