Staining Tips and photos are by Joel Terbrueggen
Pre-Staining
Most of the time, new or replacement planks are much lighter than the surrounding wood or original wood. Here is a technique that usually works well for me.
If the color difference isn’t significant this 1st option sometimes works. After sanding and fairing the area with 60 grit followed by 80 grit and no more than 100 grit, re-sand the lighter wood with 60 grit then stain the boat. The coarser sanding allows more of the filler stain into the grain resulting in a darker plank.
More often than not, the difference is too great for the first suggestion. Then we have to get more aggressive with the coloring of the lighter plank. After sanding and fairing the area, tape off the lighter plank/wood. Now apply a coat of Minwax Red Oak #215. This process is done using a chip brush and wiping off with an absorbent rag. Old t-shirts work well for this. The degree of darkening the wood is determined by length of time the stain is on before wiping off. Immediately remove the tape and apply the filler stain. The colors will blend then. I like to refer to this technique as “instant aging”. Now finish as usual. 
Staining
Staining- It is the most important aspect of refinishing.
Mix the filler/stain to a consistency of a very thin paint. Apply to the wood with a brush or roller. I like to use a 6” roller and a 2″ or 3” chip brush. 
Remove the stain before it can dry by wiping with a plastic scraper (Bondo scrapers work well) followed by a rough cloth (burlap works best). Rub in a circular motion to fill in the grain, then finish rubbing with the grain. DO NOT ALLOW THE STAIN TO DRY BEFORE WIPING. It is helpful to have a spray bottle with paint thinner in it close by. If the stain is too thick or dries, spray some thinner on the burlap (NOT ON THE WOOD!!) and rub it out. Spraying thinner on the wood can cause runs. 
When two-tone staining, tape off the area to be stained lighter and stain that area first. Apply two coats of sealer then stain the darker wood. This way if any of the darker stain splatters onto the lighter stain it can be easily wiped off. 
Sealing
Sealing- Follow staining with at least two coats of sealer. I will LIGHTLY sand with 220 grit or a Scotch Brite pad. I just want to break down the gloss for adhesion with the next coat.
Next are the deck seams.
Joel Terbrueggen is a member of the Ohio Valley Chapter of ACBS. He has presented many restoration lessons which are available in the Video Library available on our ACBS Members Only site under the Resources tab. Joel also donated his extensive library of cataloged photos taken as he performed surveys on antique and classic boats over a 16 year period. These are also in the ACBS Members Only site under the Resources tab. Joel Terbrueggen currently does much of the wood restoration on boats at the Motor Boat Garage in Cincinnati, Ohio.
Watch for more tips from Joel in the future.
Have you kept a log of the restoration of your boat? Please share it with some pictures.
I have found that using clear shellac cut 50% with alcohol and sanded after drying will make the porosity of the wood the same as for old and new wood. You must sand all wood as noted in article. When the stain is applied no dark and light areas are showing.
We used this technique 40 years ago on doors of birch and oak to make color uniform after staining.
Worked for me on wood boats I have done.
Walter,
Thanks for the information. I am always open to new ideas and suggestions. I know of too many restorers that feel there is only one way to do something.
I also use Shellac for various jobs on a boat, not a lot but it is helpful at times, especially where someone has used silicone.
Please look at some of my other tips on this site. Just enter my last name in the search box and several will come up. Perhaps you will see something there that can be expanded on as well.
Joel