As for the blemishes and refinishing... I suggest sanding the entire body down to bare wood... This will get rid of any dings that have only affected the finish... and leave you with the much more shallow dings that made it through to the wood... With these, you shouldn't need to use any filler... I would first use a damp rag and a soldering iron to steam out any dings... This is done by placing the damp rag over the tip of the soldering iron and placing the tip where the ding is... This add moisture to the wood... expanding the area... and retracting the ding... Then when the wood dries it should be back to normal... You may want to run the sander over it once more just to make sure it's not expanded out too much... Then you're ready to apply a primer and finish... or dye... or whatever you choose to use.
For replacement necks check out warmoth... they can be pricy but it's not easy to find bolt on necks that don't have a standard Strat heel... which is the most common kind of bolt on... The strat heel is rounded... where as yours is square... Warmoth offers different heel shapes, spacings, radius', as well as you can have them finish the neck....
Good luck.
