Depending on what you mean by the what you said, the quotes will vary considerably. I'd recommend you do as much of the work as you can, as the labor prices at most boat yards are running north of $85-100 PER HOUR. Finding a yard that allows you to do the work will be a problem in many areas.
Standing rigging is relatively simple to do. What I recommend is you drop the mast and take your rigging, assuming it is basically intact, and ship it to Riggingonly.com in Fairhaven, MA. They can make up replacement rigging for it based on what you send them. I would highly recommend you get the shrouds and stays a bit long and have the top terminals swaged and use Hayn HiMod mechanical fittings for the bottom and terminate them yourself.
As for the caprail replacement... that can vary a lot, depending on how it is fastened and what it is made of.
Re-wiring the boat is primarily labor... the material costs aren't all that expensive compared to the labor involved. I'd recommend buying the wiring, crimper, crimp terminals and such and doing it yourself. Maine Sail has an excellent tutorial page on Marine Wiring Termination that you should definitely read.
As for removing the bottom paint, one of the most cost-effective ways to do this is to have someone sodablast the boat. It is reasonably inexpensive to have done. Properly done, it leaves the surface ready for fairing, barrier coating and bottom painting. I'd point out that unless there are some really gross problems with the bottom's condition, fairing it isn't going to help all that much, since a Southern Cross 31 is not a fast boat, and no amount of fairing will help it much.
Barrier coating is pretty easy to do yourself. I wrote this post about using Interprotect 2000E to barrier coat, and alternating the colors to make it easier to do neatly.
Alternating the colors helps a lot with determining where you've painted, but it is also very useful for helping you coat the areas around the boat stands. For instance:
The first layer is gray, since the gelcoat is white, and you can paint right up to the boat stand pads. Then you paint a layer of white, and leave about a two-inch margin of gray paint around the pads... then paint a layer a gray and leave a four-inch margin around the pads or about two-inches of white and two inches of gray showing...and then finish with a layer of white—with a six-inch margin around the pads—with two inches of gray, two inches of white and two inches of gray.
Then when you move the boat stands, you can fill in the pads and layer the paint accordingly... adding gray to cover the white square left by the pad.. then white to cover the gray square, and so on.
Also, by alternating colors, you can see if someone has sanded through the barrier coat when you're prepping the boat for re-painting. If there's an area that is gray or grayish, they've sanded through at least the outermost layer of barrier coat. If you had all white, you wouldn't be able to tell if they had sanded down through the barrier coat as easily—if you had all gray, you could tell they sanded through the barrier coat...but not if they've sanded into it...
I hope this helps clear things up a bit.
I would point out that if you're going to barrier coat, you'll probably want to "hot coat" the bottom paint to the barrier coating. This requires you apply the paint when the final layer of barrier coat has reached the "thumbprint" stage of cure. Use a different color for the first layer or two of bottom paint, especially if you're using an ablative, so that you can tell when the paint is wearing thin.
Maine Sail has an excellent tutorial on installing/replacing through-hulls
Looking for costs associated with replacing the following items. I would like both DYI costs and/or yard costs as I'll be deciding what to do myself and what to have a yard do.
1. Standing rigging replacement
2. Caprail replacement
4. remove bottom paint, fare, and barrier coat.
5. Thru hulls
Also need recommendation for a boatyard in the Tampa/St Pete area that could do some/all of the work.