I can't help with the costs involved, but I can help a bit with the process...
Best way to have the bottom paint removed is by media blasting - in most cases, that would be soda blasting.
Companies will come to you (or your marina), and remove the bottom paint with either walnut shells, or baking soda.
Once the paint has been removed, you aren't done.
When the bottom was prepped for bottom paint, it was probably sanded with 60 or 80 grit paper to remove the mold release wax, and give the surface some 'tooth' that the paint would stick to.
To take it back to factory fresh, the bottom would have to be wet sanded beginning with maybe 400 grit, and ending with maybe 2000 grit.
I say 'maybe' because each job is different, and it all depends on how smooth and perfect you want it to be.
Can it be done? Absolutely! However understand that the process is time and manpower dependent.
We have owners here who have done this job with their boats, so hopefully some of them will weigh in and help you out.
As for the repair of the washboards where the down riggers were mounted, again, no big deal.
Members here have discovered that fiberglass repair is easier than it looks, and there are some great results in the "Projects" section.
If you don't care to do the job yourself, any decent marina has fiberglass guys who can make it look just like new.
If you decide to go ahead with this project, grab your camera, document the job, and post it in the Projects area!
Good luck!